Northern Illinois overcame a halftime deficit with a late 21-point flurry to improve to 10-0 and to 6-0 in the Mid-American Conference's West Division. Ball State would have won the division title if it had upset the Huskies, but Lynch came through with a series of clutch plays in the final period to decide the contest.
Ball State fell to 9-2 for the season and to 6-1 in league play. Toledo, having just one conference loss, is still in the hunt for the division title and will host Northern Illinois next week.
The winner of the West Division will meet either Buffalo or Bowling Green for the conference title in Detroit on Dec. 6.
The game was tied midway through the fourth period when Lynch was hit behind the line of scrimmage twice on third down, but he avoided the sack and found Matt Williams with a 25-yard pass to the Ball State 38.
Two plays later Lynch hit Da'Ron Brown with a 36-yard touchdown pass that gave Northern Illinois a 34-27 lead.
The Huskies then stopped Ball State on a fourth-and-1 play at the Northern Illinois 44 and Lynch next drove his team to another touchdown, which he scored on a 16-yard run with 2:25 left.
Northern Illinois tacked on yet another score with 46 seconds to play on a 49-yard interception return by Joe Windsor.
Lynch completed 26-of-32 passes for 345 yards and two touchdowns without an interception. Ball State's Keith Wenning went 35-of-49 for 324 yards.