MINNEAPOLIS — Christian Ponder didn’t flinch against that feisty, swarming San Francisco defense.

Minnesota’s flourishing young quarterback engineered a stunning victory after two of his more-decorated division peers fell well short. Ponder threw two touchdown passes to tight end Kyle Rudolph and ran for another score to help the Vikings hand the 49ers their first defeat, 24-13 on Sunday.

“It’s big, more for people outside this organization than us. We’re already confident in what we can do,” said Ponder, who went 21 for 35 for 198 yards and, most importantly, no turnovers or sacks.

After a dominant start to their NFC North tour by decisively beating playoff teams Green Bay and Detroit, the 49ers (2-1) were beaten in every way by the team least likely to do so.

Aaron Rodgers of the Packers and Matthew Stafford of the Lions each had a pass picked off in their game, and they were harassed often by a defense that’s been one of the NFL’s best for the last several seasons. Ponder, in his second year and in the long shadow of Rodgers, Stafford and Chicago’s Jay Cutler in this pass-driven division, deftly avoided the rush and made a bunch of clutch throws on the run.

“It’s huge for the rest of our season. It’s a springboard,” Rudolph said.

The Vikings (2-1) began the game boldly with a fourth-and-goal touchdown pass by Ponder to his favorite target, Rudolph. They finished strong by forcing three turnovers and two punts in a wild, drawn-out fourth quarter due in part to more replacement referee blunders. Twice in a six-play span, the 49ers were allowed to withdraw a called timeout to challenge a play instead. The first one was reversed, a fumble by Toby Gerhart given to the 49ers after video review.

But the Vikings played so well that didn’t matter. Neither did Gerhart’s second fumble a few minutes later.

“You can’t think that the game’s just going to be given to you, especially when you guys are hyping us up and saying we’re that good,” 49ers linebacker NaVorro Bowman said. “Everyone is trying to knock us off. You just have to be prepared for it every single game.”

Playing against his former team in the regular season for the first time, Randy Moss had a quiet afternoon with three catches for 27 yards. Frank Gore managed only 63 yards on 12 carries, and Alex Smith’s franchise-record interception-free streak ended at 249 passes when Vikings rookie Josh Robinson picked him off with 2:18 left.

Donte Whitner dropped a sure interception and a potential touchdown midway through the fourth quarter after Vikings receiver Michael Jenkins slipped on third down. David Akers had a 43-yard field goal blocked by Letroy Guion late in the first half. And Smith lost a fumble on a late sack by Jared Allen.

“I know the Vikings have always played teams tough, especially when they’re an underdog. That’s Minnesota football,” Moss said.

“We’ll keep going back at it.”

Smith finished 24 for 35 for 204 yards. He found tight end Vernon Davis on consecutive passes, the second one a 1-yard play-action fake, in the third quarter to pull within 17-13. The Vikings blew 17-0 and 20-0 halftime leads last September in losing consecutive home games to Tampa Bay and Detroit, and this was starting to set up the same way.

But with one third-and-goal pass by Ponder — Adrian Peterson was wide open next to Rudolph, who reached around Whitner for it — the lead was back to 11. The Vikings were on their way to burying that painful start to last year’s 3-13 record. That drive was fueled by three 49ers penalties, including two unnecessary roughness calls, one by Dashon Goldson against Rudolph.

“Knock on wood, but he’s playing some of the cleanest football I’ve ever seen somebody play at any age in the NFL,” said Vikings linebacker Chad Greenway, who had two sacks. He added: “He just has that poise about him.”

Peterson finished with 86 yards on 25 grueling carries, helping give Ponder some room to throw. The Vikings went 82 yards in 16 plays to start the game, but Peterson was stonewalled for 1 yard on second-and-goal at the 2 and no gain on third down. With inches to go, Ponder rolled left under pressure by Goldson and threw a floater off his back foot that Rudolph ran down in the corner of the end zone for a 7-0 lead. Rudolph had four catches on that drive.

Then Ponder used his feet, taking off three times for 34 yards on a second-quarter possession, including the 23-yard sprint that made it 14-3. Accelerating off a cut inside the 10, perhaps reminding 49ers fans inside the dome of their old favorite Steve Young, Ponder dived across the goal line for the final yard.

“There was a big running lane, and I figured that if my … legs were fast enough, maybe I’d get there,” Ponder said. “And I got there, so it was good.”

NOTES: Moss moved past Tim Brown into fourth place on the NFL’s all-time receiving list with 14,946 yards. … Vikings FS Mistral Raymond’s right ankle rolled awkwardly while trying to tackle Gore at the end of the first quarter. He left on a cart and was on crutches afterward. “From the naked eye, it looks like a very serious injury,” Frazier said, “but I don’t know all the details.” … 49ers LB Patrick Willis walked gingerly off the field with an injury to his lower right leg and DT Isaac Sopoaga hurt his lower left leg in the fourth quarter. Harbaugh said both players would be X-rayed and re-evaluated. … The 49ers play the Bears at home on Nov. 19. … Gore passed Roger Craig for the most career rushing attempts in 49ers history. … Percy Harvin led the Vikings with nine catches for 89 yards.