The first of those two scores was a 60-yarder that capped a 17-point third quarter for the Falcons (3-3, 1-1), who trailed 10-0 at halftime.
Bowling Green held the Zips (1-5, 0-2), who gained 280 first-half yards, to 36 in the second half.
Anthony Samuel, who carried 15 times for 117 yards, started the Falcons off quickly in the third quarter with runs of 27 and 20 yards on the first two plays from scrimmage. Bowling Green had 144 rushing yards in the third quarter as it won for the 500th time in the program's 94 seasons against 349 losses and 51 ties.
Akron's Dalton Williams, who was averaging 335.8 yards passing, was held to 228, completing 29 of 50, including a touchdown.
South Carolina's loss to The Citadel, coupled with Georgia and Florida struggling in tight victories, was an embarrassment for the conference.
Ryan Graham pass complete to Kenny Golladay for 27 yds for a TD (Christian Hagan KICK)
Ryan Graham pass complete to Juwan Brescacin for a loss of 4 yards to the NoIll 17
Riley Neal pass complete to Chris Shillings for 7 yds for a TD
Chase Herbstreit finishes up the regular season going with Ohio State to knock off Michigan, which doesn't come as a shock to the family.
Oklahoma is projected to be in the College Football Playoff after the release of the CFP rankings, while West Virginia joined the bowl-eligible crowd.