Kanon Woodill made it a two-score game when made a 27-yard field goal with 6 minutes left. Earlier, Woodill made kicks of 46 and 21 yards.
Northern Illinois (4-2, 2-0 Mid-American) has won two straight following consecutive defeats after its historic 16-14 win over Notre Dame in South Bend, Indiana.
Bowling Green (2-4, 1-1) led 7-3 when Connor Bazelak threw an 11-yard scoring pass to Harold Fannin Jr. with 6:55 left in the first quarter.
With the win, Northern Illinois evened the all-time series record at 12-12.
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