Justin Gildea scored on a 26-yard fumble return on the last play of the game for the Owls. There was a penalty on the play and it took nearly 15 minutes for officials to sort out if the score would stand.
McManus also kicked field goals of 53, 44 and 40 yards in front of more than 32,000 fans, the second-largest crowd to watch the Owls in Lincoln Financial Field. The Owls won the Mayor's Cup presented to the winner of this series.
The Owls went ahead 22-21 on Chester Stewart's 62-yard TD pass to Michael Campbell. Stewart fumbled the snap on the next possession and the Wildcats recovered inside the 25. Nick Yako kicked a 41-yard field goal with 1:56 left that put Villanova up 24-22.
The Owls had circled the date of this game since the schedule was released after the Wildcats beat them last season. Coach Al Golden was quick to note that of all of Temple's milestones last year - first winning season since 1990, first bowl game since 1979 - the Owls failed to beat city rival Villanova.
For most of this one, it looked like the Wildcats would win for the fourth straight time. Villanova's Chris Whitney completed 15 of 17 passes in the first half and finished 17 of 25 for 133 yards with two touchdowns.
His first TD pass was a 3-yarder to Matt Szczur, the Most Outstanding Player in the FCS title game. The two-sport star was drafted by the Chicago Cubs and had a 21-game hitting streak in the minors this year.
Villanova coach Andy Talley rested Szczur to get him fresh for the grueling season ahead. He caught five passes and even completed one.
Aaron Ball's 9-yard run gave Villanova a 14-7 lead in the second quarter.
McManus ended the half with a 54-yard field goal, the second-longest in Temple history. Don Bitterlich hit a 56-yarder in 1975. McManus had plenty of oomph as the ball would have been good from at least 5 more yards out.
The Owls needed all of McManus' kicks to eek out this victory. He hit one in the third quarter and another in the fourth that brought the Owls within five.
Stewart, who made four starts last year, made a perfect pass to Campbell to put Temple ahead. The Owls botched the 2-point conversion. Stewart was 16 for 27 for a career-high 200 yards. Campbell had eight catches for 127 yards.
Years of futility had eroded Temple's fan base until Golden revitalized the program. Fans tailgated outside the Linc, home of the NFL's Eagles, hours before the rare 5 p.m. kickoff. Only a Penn State game in 2007 ever drew more fans.