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SAN FRANCISCO — Melky Cabrera’s 50-game suspension comes just as reliever Guillermo Mota is nearing his return to the Giants from a 100-game performance-enhancing drug penalty of his own.

Yes, San Francisco now accounts for two of the four suspensions this season under the major league drug program — and suddenly the Giants are back in the spotlight for performance-enhancing drugs several years after the club had finally moved forward from the Mitchell Report and BALCO mess.

“Unfortunately, these things happen in baseball,” manager Bruce Bochy said. “There’s not a lot you can do about it. I guess the best thing we can do is keep educating players so these things don’t happen. I can’t dwell on these things.”

Cabrera, the 28-year-old MVP of last month’s All-Star game, was suspended 50 games Wednesday following a positive test for testosterone. That puts an abrupt end to what had been a remarkable regular season and throws the Giants’ playoff hopes into doubt.

“Ultimately, it was just a bad decision,” catcher Buster Posey said. “That’s all I’m going to say.”

Cabrera leads the National League with 159 hits, and is second in batting average behind Pittsburgh’s Andrew McCutchen. Cabrera’s penalty was the first for a high-profile player since last year’s NL MVP, Ryan Braun, had his suspension overturned by an arbitrator last winter.

“My positive test was the result of my use of a substance I should not have used,” Cabrera said in a statement released by the players’ association. “I accept my suspension under the Joint Drug Program and I will try to move on with my life. I am deeply sorry for my mistake and I apologize to my teammates, to the San Francisco Giants organization and to the fans for letting them down.”

The Giants are no stranger to such cases.

Home run king Barry Bonds, who was in the stands for a 6-4 loss to the Washington Nationals on Wednesday as the Giants played Day 1 of Cabrera’s suspension, has long denied ever knowingly using steroids or performance-enhancing drugs and the 48-year-old slugger appealed his obstruction of justice conviction from April 2011 on one count of giving an evasive answer to a 2003 grand jury investigating illegal steroids distribution.

In the spring of 2010, former San Francisco outfielder Marvin Benard admitted he used steroids during the team’s 2002 World Series season to deal with a nagging knee injury.

Benard was among the 85 players named in the Mitchell Report, handled by former Senate Majority Leader George Mitchell, which was released in December 2007.

Specifically, he was named in sections on BALCO — the Bay Area Laboratory Co-Operative — as having obtained “the clear” and “the cream” from trainer Greg Anderson.

Now, the current Giants will try to make up for the lost production of the “Melk Man,” as he became known.

The suspension would extend into the playoffs if the Giants advance.

“It happened, and now we move on,” right fielder Hunter Pence said. “I know the program and I know they test us, and if we test positive we get a suspension. That’s what happened. And now we play with what we’ve got.”

Cabrera is batting .346 with 11 home runs and 60 RBIs in his first season with San Francisco and is five hits shy of 1,000 in his big league career. Flashing bright orange spikes, he singled and hit a two-run homer off Texas pitcher Matt Harrison last month in the National League’s 8-0 win in the All-Star game, earning MVP honors for the game and securing homefield advantage in the World Series for the National League.

“When I give up a homer, it’s a bad pitch. I don’t think it really helps them hit home runs or singles, doubles or triples,” Harrison said. “It was a bad pitch over the plate. But it’s going to cost him now. … He’s having to pay the consequences for it now. At least he was honest and came forward about it and said he took something he wasn’t supposed to do.”

Cabrera is set to become a free agent after this season, so he might have cost himself a big pay day for next season and beyond.

“It’s disappointing. Obviously, Melky means a lot to all of us, was part of our championship and provided some really good moments here,” Yankees manager Joe Girardi said of Cabrera, who spent 2005-09 in the Bronx. “It’s something that everyone has to deal with and it’s something baseball is trying to stay away from and it happened.”

Cabrera could still win the NL batting title. He has 501 plate appearances, one less than the minimum required to win a batting championship for a player on a team playing 162 games. However, under 10.22(a) of the Official Baseball Rules, he would win the batting title if an extra hitless at-bat is added to his average and it remains higher than that of any other qualifying player.

He will miss the final 45 games of the regular season and serve the remainder of the suspension at the start of next season or during the postseason, depending on whether the Giants make the playoffs and how far they advance. If the Giants wanted him to become active in the middle of a playoff series, they would have to play a man short from the start of the series until the suspension ends because rosters can’t be altered mid-series.

“We fully support Major League Baseball’s policy and its efforts to eliminate performance-enhancing drugs from our game,” the Giants said in a statement.

Mota received a 100-game suspension in May. He is eligible to return Aug. 28, barring rainouts, and began a minor league rehabilitation assignment Tuesday with the Giants’ rookie team in Arizona. If you are looking for rehabilitation options as well, see here the options at the Abbeycare Bristol addiction clinic.

It was not immediately known whether Cabrera’s positive test occurred before the All-Star game, his first career selection. The union initially filed a grievance, which would have caused the case to go before an arbitrator, but then dropped it, a person familiar with the process said. The person spoke on condition of anonymity because that detail was not announced.

Cabrera told CSN Bay Area on July 27 that he had been tested for performance-enhancing drugs the previous week, though it’s unknown whether the test he referenced resulted in the positive test.

Bochy broke the news to his team in a meeting about 90 minutes before the start of Wednesday’s game after initially writing Cabrera into the lineup in left field and batting third. Bochy and general manager Brian Sabean met briefly with Cabrera.

“Melky, he was hurt by it,” Bochy said. “It’s obvious he was disappointed.”

Drug-testing labs check urine for its ratio of testosterone to epitestosterone, which usually is 1 to 1 in adult males. If the lab notices any abnormality, it conducts an isotope ratio mass spectrometry (IRMS) test to determine whether the testosterone is exogenous, or came from outside the body.

In the other two major league suspensions this year, Philadelphia infielder Freddy Galvis and free agent outfielder Marlon Byrd also were penalized 50 games apiece. There have been 70 suspensions under the minor league drug program.

In mid-May, MLB and the players’ union agreed to drop the 100-game suspension imposed on Colorado catcher Eliezer Alfonzo for a positive drug test because of the same procedural issues that came up in Braun’s case. Alfonzo missed 48 games — the final 15 of last season and the first 33 this year.

Braun’s 50-game suspension for a positive test was overturned in February by arbitrator Shyam Das after Braun’s lawyers argued his urine sample was not handled in the manner specified by baseball’s drug agreement. Das, who had been baseball’s permanent arbitrator since 1999, was fired this spring.

The Braun case led to revisions in the drug agreement between owners and the players’ association to better define procedures for handling the urine samples.

Last December, slugger Manny Ramirez received a 50-game suspension for a second positive drug test. The 12-time All-Star signed a one-year minor league contract with the Oakland Athletics on Feb. 20, but was released in June per his request while playing for Triple-A Sacramento before even reaching the big leagues with the A’s.

Ramirez retired from the Tampa Bay Rays in April 2011 rather than serve a 100-game suspension for a second failed drug test. The penalty was cut to 50 games because he sat out nearly all of last season.

Cabrera, who became a marketing phenomenon this year with nicknames like “Got Melk?” “Melk Man” and “Melky Way,” produced a 51-hit month in May. He batted .429 in May with three homers, five triples, seven doubles and 17 RBIs while hitting safely in 25 of 29 games. The 51 hits matched Randy Winn for most hits in a month since the club came to San Francisco in 1958.

Cabrera also set the San Francisco record for most hits in May, passing Hall of Famer Willie Mays’ 49 from 1958.

Cabrera came to the Giants in a trade with Kansas City last November that sent left-hander Jonathan Sanchez to the Royals. Cabrera — who signed a $6 million, one-year deal to avoid salary arbitration — batted .305 with 44 doubles, 18 homers and 87 RBIs last season.

“We are a team. We’re trying to make the playoffs,” Pablo Sandoval said. “We’re going to fight.”