Harris also caught a scoring pass on a trick play as the Falcons clinched the Mid-American Conference West Division title. They will host Miami of Ohio on Thursday in the championship game.
The Falcons (10-2, 7-1 MAC West) were 9-3 last season under coach Urban Meyer, who left for Utah, but did not skip a beat under Gregg Brandon, their former offensive coordinator, who led the school to its first-ever appearance in the MAC title game.
Bruce Gradkowski threw a 58-yard touchdown to Lance Moore with 2:30 left to cut the lead to 31-23. After missing the extra point, the Rockets had one more chance when they recovered the onside kick, but the Rockets were unable to score.
Harris, who completed 21-of-26 passes for 256 yards, opened the scoring in the third when he caught a pass from wide receiver Cole Magner for a touchdown.