SOUTH BEND, Ind. — The NCAA announced Tuesday that Notre Dame must vacate all 21 victories from the 2012 and 2013 seasons, including the 12-0 run that vaulted the Fighting Irish into the national title game against Alabama, because a former student athletic trainer committed academic misconduct by doing substantial course work for two players and impermissibly helped six others.

The school ripped the NCAA for its decision to strip the wins, which included the best season of coach Brian Kelly’s seven years in charge of the storied program. The school said it would appeal and the Rev. John Jenkins, the university president, said the NCAA has never before vacated the records of a school that had no involvement in the underlying academic misconduct. He also noted the NCAA has since voted to change the rule that brought this case under NCAA jurisdiction rather than leaving such decisions to individual schools.

The Division I Committee on Infractions panel put Notre Dame on probation for a year and ordered a $5,000 fine, penalties the school agreed with. There were no bowl or scholarship punishments.

Kelly said he knew the vacated wins were a possibility since he and other Notre Dame officials met with the NCAA several months ago. He said he had hoped it would not come to that, saying he hoped “reasonable people would come to a reasonable decision.”

“We did the right thing. I’m proud of our support staff, our academic support staff. I’m proud of the people that represented us here at Notre Dame during this time,” Kelly said. “And if doing the right thing means that you’ve got to put an asterisk next to these games, that’s fine with me. We still beat Oklahoma. We still beat Wake Forest, we still beat all those teams, so you can put an asterisk next to it. If that makes you feel better, then that’s fine with me.”