Lynch finished off a spectacular personal performance in dramatic game that saw Kent State rally with a 21-point fourth quarter. The No. 19 Golden Flashes brought about overtime when Spencer Keith threw a 19-yard touchdown pass to Tim Erjavec with 44 seconds to go in regulation.
Both sides managed a field goal in the first overtime, but Lynch put 18th-ranked Northern Illinois in front to start the second extra period.
Kent State moved the ball to the Northern Illinois 9-yard line, but faced fourth down and the game ended when Demetrius Stone intercepted a throw by Keith.
Northern Illinois built a 31-17 lead through three quarters on the running and throwing of Lynch, who completed 19-of-34 passes for 212 yards and picked up 160 more yards on 36 carries. He accounted for four touchdowns, three of them on the ground. Lynch ran 9 yards for a score with 3:12 to play in the fourth quarter, putting Northern Illinois in front 37-30.
Akeem Daniels added 128 rushing yards and a touchdown for the Huskies, who won for the 12th time in 13 games. Their only loss this season was a one-point setback to Iowa in their opening game of the campaign.
Kent State (11-2) was led by 190 passing yards from Keith, who threw two interceptions.