Eleby and Moore connected for scores three times in the first half as Western Michigan took a 28-7 halftime lead.
Northern Illinois managed just nine first downs and 31 yards passing. The Huskies ran for 268 yards but lost two fumbles. Senior fullback Clint Ratkovich had a 96-yard touchdown run in his final home game. Antario Brown had TD runs of 44 and 41 yards.
The Huskies (8-4, 6-2) had already clinched the MAC Western Division championship and will play for the league title for the eighth time in the past 12 seasons.