The Falcons (10-3) won a MAC title for the first time since 1992 just months after Johnson was born.
Lynch was 21 of 40 for 219 yards with a TD and two interceptions, including one in the fourth quarter that set up Johnson's fifth TD that put Bowling Green up 40-20.
After Lynch threw an incomplete pass to turn the ball over on downs on the ensuing drive, he was taunted by Falcons fans: "No more Heisman! No more Heisman!"
On this night, the best QB played for Bowling Green.
Johnson was 21 of 27 for a career-high 393 yards, connected with five teammates for scores and didn't throw an interception.
Bowling Green's Travis Greene had 133 yards rushing to give him 1,555 this year, surpassing the school's single-season record set by Fred Durig in 1951. Greene had a 16-yard TD run to make it 47-20.
Alex Bayer had seven receptions for 124 yards and a TD that gave the Falcons a 31-13 lead at halftime. Ronnie Moore caught four passes for 145 yards and a TD.
Lynch was held to just 35 yards rushing in the first half and when forced to pass, he was often off the mark as he completed just half of his attempts by halftime. He seemed to throw one pass too high, but Juwan Brescacin leaped to snag the football with his left hand in the end zone to tie the game midway through the first quarter.
Tyler Tate's 25-yard field goal with 6:49 left in the first half put Bowling Green ahead for good.
Lynch ran for a TD to pull the Huskies within 11 points early in the third quarter, but they couldn't get closer.
The next two possessions ended with kickers for both teams missing field goals.
Tate made a 52-yard field goal the longest of his career by 7 yards to give Bowling Green a 34-20 lead early in the fourth quarter.
When the outcome was still in doubt, Lynch surpassed his yards rushing total from last season 1,815 and will have 1,881 yards rushing going into a lackluster bowl game.
Lynch and the Huskies lost for the first time since Jan. 1, 2013, when Florida State dominated them in the Orange Bowl.
Instead of going back to a BCS game and helping the MAC get a big check to split among its schools, Northern Illinois might end up coming back to Detroit in a few weeks for the Little Caesars Pizza Bowl.
Bowling Green 47, No. 16 N. Illinois 27
O Falcons quarterback Matt Johnson goes 21 of 27 for 393 yards and a career-high five touchdowns.
• The Huskies' Jordan Lynch breaks his own record for season rushing yards by a QB, but also throws two interceptions.