He dropped back, waited until he spotted an opening and scrambled up the middle for a first down that sparked a 99-yard drive, clinching a 35-17 victory over Toledo on Wednesday night.
The No. 20 Huskies also secured a fourth consecutive trip to the Mid-American Conference title game.
Lynch, their do-it-all quarterback, said he never felt rattled, even with little room for error. That's because he said the Huskies practice those 99-yard drives.
"That's a momentum killer," he said. "It's a real dagger to the defense."
Lynch finished with three touchdowns -- all in the second half -- and 161 yards. The third score on a 1-yard dive came at the end of the Huskies' long drive in the fourth quarter.
He ran for 62 yards on seven carries during the drive, the big play coming when he scrambled out of the end zone to pick up a first down.
The Huskies (11-0, 7-0 MAC) extended their 24-game conference winning streak and are off to the best start in school history.
Lynch was 17-of-22 for 202 yards passing and ran for 161 yards on 28 carries. He is 23-2 as a starter.
Northern Illinois is still in the hunt for a second straight Bowl Championship Series appearance after playing in the Orange Bowl last season. The Huskies are 16th in this week's BCS rankings.
They need to keep winning and move ahead of Fresno State in the standings to keep their hopes alive.
Northern Illinois is the first MAC team to appear in four straight league championship games since Marshall did it six seasons in a row from 1997-2002. The Huskies have won the past two MAC titles.
The Huskies' offense sputtered in the first half without their two leading receivers, Tommylee Lewis and Da'Ron Brown, because of injuries. Lewis didn't dress for the game and Brown went out in the first quarter with an injured toe.
Toledo (7-4, 5-2) shut down Lynch too, holding him to just 30 yards on the ground in the first half.
But there was no panic.
Huskies coach Rod Carey said all he had to do was remind his team to finish their drives.
"That calmed the guys down," Carey said.
One guy he wasn't worried about being rattled was his quarterback.
"He's pretty decisive," Carey said. "When he's running and making plays, that's just him."
Lynch's second touchdown came when he faked a handoff and raced up the middle for a 31-yard touchdown, pulling the Huskies ahead for good at 21-17 with 6:15 left in the third quarter.
"He's always poised," said receiver Juwan Brescacin, who had eight receptions for 121 yards. "That's why we're as good as we are."
Lynch has thrown for at least 200 yards and run for 100 in the same game 11 times in his career. He moved into third place on the school's rushing list behind Garrett Wolfe and Michael Turner, both of whom went on to the NFL.
Terrance Owens threw two touchdown passes for Toledo.
Toledo's leading rusher, David Fluellen, started after missing the past two games with what the team has called a lower leg injury, but he was held to 54 yards on 15 carries -- far below his 133-yard average.
The Rockets led 10-7 at the half after Owens found a wide open Alonzo Russell along the right sideline for a 45-yard touchdown, putting Toledo ahead.
The Huskies drove 85 yards on the opening possession of the second half to take back the lead 14-10, scoring on a 12-yard run by Lynch, his first of the game.
Owens came back with a 36-yard touchdown to Bernard Reedy, who stretched out to make the catch in the back of the end zone, pulling the Rockets ahead 17-14 midway in the third quarter.
Mississippi's football program has been cited for 13 of the 28 NCAA rules infractions included in the notice of allegations that the Rebels received in January.
ESPN Big Ten reporter Brian Bennett discusses why the SEC is upset about Michigan's spring break trip and what the NCAA might do about it.
Stanford and Notre Dame split their last two meetings in dramatic contests, and their 2016 matchup will be highly anticipated.
A lawsuit alleges that the University of Tennessee has violated Title IX policies and created a "hostile sexual environment" through indifference toward sexual assaults by student-athletes.
Ian O'Connor, senior writer at ESPN.com, joins The Paul Finebaum Show to discuss Roger Goodell's response to safety concerns in the NFL.
Stanford defensive line coach Randy Hart is retiring after 46 years as a college coach.