Safety Tom Zbikowski returned a fumble for a 25-yard touchdown for Notre Dame and Travis Thomas - the starting linebacker - set up his own 1-yard TD run with a 43-yard run on a fake punt.
After being held without a touchdown pass against Georgia Tech, Quinn threw for three touchdowns and 229 yards in the first half against the Nittany Lions, leading the Irish to a 20-0 halftime lead.
He still overthrew a few open receivers and had a few passes dropped, but finished 25-for-36 for 287 yards. Through two games he has 533 yards passing - well ahead of last year's pace of 367 yards.
Anthony Morelli, making his second career start for the Lions, found playing on the road a little more difficult. He was 21 of 33 passing with one interception and a fumble. He did have a 2-yard TD pass to Deon Butler with 5:51 left. Reserve quarterback Darryl Clark scored on a 5-yard run with 20 seconds left.
The difference in the game was that Notre Dame was able to overcome its mistakes, while the Nittany Lions could not. The Irish again struggled early with penalties, two that stalled drives. Then Zbikowski couldn't handle a punt, but it bounced forward and Raeshon McNeil recovered for the Irish.
The Nittany Lions, though, couldn't overcome their problems. They had a botched field-goal attempt on their first possession. Then Tony Hunt fumbled the ball on Penn State's second possession and Ronald Talley recovered for the Irish. On their first possession of the second half, Irish linebacker Maurice Crum Jr. knocked the ball loose when he hit Morelli. Zbikowski picked up the ball and returned it for a touchdown.
Chinedum Ndukwe had an interception and a hard hit on Derrick Williams, forcing a fumble, on one of several plays when the receiver lined up at quarterback.
The Irish special teams contributed as well. Carl Gioia, who missed both his field goal attempts against Tech a week earlier, kicked two from 35 yards, and Geoff Price had a 62-yard punt.
The all-around performance at home was welcomed by the Irish, who were 10-8 at home the previous three years and lost their first two home games under Weis last season.
A year ago heading into his first home game, Weis tried to shield his players from what he termed the "circus." Now he calls home games events and plays up to the crowd.
The Friday night pep rally, which players attend, was moved to Notre Dame Stadium so 35,000 fans could attend and fans entering the stadium Saturday were given green towels that read "9-3 is not good enough" - the same saying Weis had hanging in the team weight room during the offseason.
It was a disappointing performance for the Nittany Lions who were eager to show they were ready to be national contender again. The victory gives Notre Dame a 9-8-1 edge in the series, with the two teams meeting again next season in State College.
It was the first meeting between the two storied schools since Penn State joined the Big Ten in 1993.