Northern Illinois had gone 12-0 during the regular season and became the first MAC team to defeat two Big Ten schools in the same year.
The Huskies, however, ran into a hot quarterback and found themselves in a 31-13 hole at halftime.
Johnson threw for 181 yards and two scores in the first period alone and finished with 21 completions in 27 attempts for 393 yards. He was not intercepted.
Five different receivers scored for the Falcons with Johnson's first-period touchdown throws going to Tyler Beck for 28 yards and Ronnie Moore for 36.
Bowling Green broke the game open during the latter stages of the first half with Johnson connecting on scoring throws of 22 yards to Heath Jackson and 12 yards to Alex Bayer.
Johnson's final touchdown pass was a 5-yarder that he flipped backhanded to Travis Greene as the Bowling Green quarterback was on the verge of being sacked.
Greene also ran for 126 yards with a rushing touchdown while Moore and Bayer combined to catch 269 yards worth of passes.
The outcome left Florida State and Ohio State as the only two unbeaten teams in major college football.
Bowling Green (10-3) compiled 586 yards of offense to 453 for Northern Illinois. Jordan Lynch completed 21-of-40 passes for the Huskies. He threw for one score and was intercepted twice.