Lynch was 5-for-17 passing and ran the ball 27 times to close out the perfect season for the Huskies (12-0, 8-0 MAC), who also have won 26 consecutive home games.
The victory put Northern Illinois in the MAC championship game against either Buffalo or Bowling Green and likely improved the dark-horse Lynch in the Heisman Trophy sweepstakes.
Darevon Chance and Antoin Scriven both scored rushing touchdowns for the Broncos (1-11, 1-7), who lost their third in a row.
Chance ran it in from 1-yard out to tie the score 7-7 with 11:09 to play in the second quarter, but Northern Illinois scored three touchdowns and two field goals by Mathew Sims and led 33-7 early in the fourth quarter.
Swim Week Miami Beach 2014 [PHOTOS]