He got help from Da'Ron Brown, who hauled in the two TD passes and finished with six receptions for 128 yards.
Hare, who didn't play until the second half, completed six of 10 passes for 109 yards and had 11 rushes for 31 yards. Hare was the third quarterback to play for the Huskies.
NIU (2-0) is 5-3 versus Big Ten teams since Sept. 19, 2009. The Huskies also lead the nation with 16 straight road victories (games played in opponents' stadiums).
Trevor Siemian was 27 for 41 for 268 yards with a touchdown and an interception for Northwestern before leaving the game with an apparent right leg injury after a late hit with 3:15 left in the game.
Northwestern is 0-2 for the first time in coach Pat Fitzgerald's nine seasons. The Wildcats lost 31-24 to California in their opener last week.
The Wildcats amassed 394 yards of total offense but most of their drives were stalled by mistakes - a dropped pass, a penalty or a sack.
It was the first meeting between the schools since 2005 when Northwestern posted a 38-37 win in a wild finish. NIU scored with 6 seconds left and could have opted for a tying extra point, but then-coach Joe Novak called for a two-point conversion that failed.
It was the Huskies' first win in eight meetings between the schools. Northwestern had posted six wins and a tie in the previous seven games.
Considering both schools' history of high-powered offenses, a shootout would have been the logical expectation. But the first half was scoreless with each team squandering its lone scoring opportunity.
The Huskies got the ball to start the second half and Hare took over the offensive reins. He immediately led NIU on a 10-play, 60-yard drive - the key play being a 25-yard pass to Brown - to set up a 32-yard field goal by Wedel for a 3-0 lead with 11:55 left in the third quarter.
After showing flashes, the Northwestern offense finally put together a complete drive on its second possession of the second half. Siemian capped a four-play, 60-yard drive with a 19-yard TD pass to wide receiver Kyle Prater for a 7-3 lead with 4:51 remaining in the third. All four plays were completed passes and the drive took just 58 seconds.
NIU, though, answered with a 13-play, 82-yard drive capped by an 18-yard scoring pass from Hare to Brown for a 10-7 Huskies lead with 52 seconds to play in the quarter.
The Huskies stretched the lead to 16-7 (the extra point failed) when Hare and Brown hooked up again, this time on a 59-yard scoring pass with seven minutes to go in the game.
On the next NIU possession, Hare scored on a four-yard run to make it 23-7.