Texas and Ohio State, with 898 wins, are now second only to MI, who has 943 wins. Texas (898) moves from a tie for 3rd place on the list, along with Ohio State, to a tie for 2nd place.
Notre Dame's all-time victory total drops from 906 to 885 with the ruling.
"Let me be clear that we in no way excuse the very serious instances of academic dishonesty committed by our students", Notre Dame president Rev. John I. Jenkins wrote in a letter responding to the NCAA's decision. The ruling stems from the academic violations of nine players during those seasons, eight of them with the assistance of a former student-athletic trainer.
The NCAA stripped Notre Dame of 21 victories, fined the school $5,000 and placed it on one year's probation in November 2016. That same athletic trainer was additionally involved in giving impermissible academic benefits to six other players.
Jenkins said had Notre Dame merely expelled the students instead of recalculating grades, had a statute of limitations for past offenses or chose not to punish the students, an NCAA penalty would not have been imposed.
Nevertheless, the decision wipes the Irish's undefeated regular season from 2012 off the books, as well as the team's 9-4 campaign in 2013 that included a win over Rutgers in the Pinstripe Bowl. On their own, Notre Dame moved to suspend five players for academic misconduct prior to the start of the 2014 season. In the letter, Jenkins said Notre Dame is "deeply disappointed" by the NCAA's denial.
"The NCAA has not chosen to ignore academic autonomy; it has instead perverted it by divorcing it from its logical and necessary connection to the underlying educational objective", Jenkins wrote. It is to the imposition of this discretionary penalty that the University objects and which it appealed.More news: Uber will force drivers offline after 12 hours to combat 'drowsy driving'
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However, that did not mean that its epic 34-31 win at Notre Dame in 2005 was now a "victory" for Notre Dame. "The committee failed to provide any rationale for why it viewed the (student trainer) as an institutional representative in our case", Jenkins wrote.
"When reviewing infractions cases, the Committee on Infractions uses the bylaws and interpretations contemporaneous to the conduct being reviewed", the appeals committee wrote. Student-to-student cheating is not normally within the NCAA's jurisdiction, but the NCAA concluded that the student's role as a part-time assistant trainer made her a "representative of the institution" and justified a vacation of team records penalty in this case.
The NCAA's announcement denying the appeal can be read here.
In its decision, the appeals committee highlighted that as a member of the NCAA, the university is subject to the Association's rules, including those related to academic misconduct and the ability to impose penalties for academic misconduct violations.
"To impose a severe penalty for this retroactive ineligibility establishes a unsafe precedent and turns the seminal concept of academic autonomy on its head".