The two defensive touchdowns came in handy on a day when the Wildcats' quarterback duo of Kain Colter and Trevor Siemian were held to a combined 122 passing yards on 10-for-17 efficiency.
Colter ran the ball 12 times for 38 yards and a score for the Wildcats (4-0), who managed just 373 total yards of offense in their final tune-up for Big 10 Conference play.
Mike Trumpy led Northwestern's ground game with 94 rushing yards and a score on 17 carries.
Maine (3-1) was paced by Marcus Wasilewski, who went 25-of-40 through the air for for 237 yards, two touchdowns and a pair of pick-offs.
Nigel Jones picked up 73 rushing yards with a score for the Black Bears.