Northern Illinois, one of six unbeaten teams remaining in major college football at 11-0, clinched a spot in the Mid-American Conference championship game. A win next week over Western Michigan will complete a perfect regular season for the Huskies along with an undisputed West Division title.
Lynch ran 12 yards for a score on the opening possession of the third quarter to overcome a 10-7 halftime deficit, but Toledo regained the lead on a 36-yard throw from Terrance Owens to Bernard Reedy.
Lynch then drove the Huskies 65, 94 and 77 yards to wrap up the victory -- running 31 yards for a touchdown at the end of the first of those drives and finishing off the second with a 1-yard run.
James Spencer produced the final Northern Illinois touchdown with a 9-yard run.
Lynch completed 17-of-22 passes for 202 yards and ran for another 161 yards and three touchdowns on 28 carries.
Toledo fell to 7-4 for the season and is 5-1 in the West Division.
Despite turning the ball over three times in the first half, the Rockets were able to take the lead at intermission thanks in part to two missed field goals by Northern Illinois' Mathew Sims.
Owens went 17-of-29 for 235 yards with two touchdowns and two interceptions.
Northern Illinois stayed unbeaten along with Alabama, Ohio State, Florida State, Baylor and Fresno State.
The Huskies will meet either Buffalo or Bowling Green for the conference title in Detroit on Dec. 6.