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Andre Harris scored on a 1-yard touchdown run to cap a 13-play, 89-yard drive with 5:20 left to give the Bears the victory.
South Dakota (3-5) trailed 14-0 with 13:16 left in the first half before rallying. Noah Shepard threw for one touchdown and ran for another and Dustin Nowotny kicked a field goal to give the Coyotes (3-3) a 17-14 lead early in the third quarter.
After taking the early lead, Northern Colorado (3-6) couldn't generate much offense until early in the fourth quarter.
Pinned at his own 11, Waggener directed the game-winning drive, which was aided by a 15-yard pass-interference penalty that gave the Bears a first down at the Coyotes' 26.
Harris scored five plays later to give Northern Colorado the lead.
South Dakota, which had scored touchdowns on two long drives, drove to the Bears 42 on its ensuing possession, but Logan Zabel intercepted Shepard at the 25. After holding Northern Colorado, the Coyotes got the ball back at their own 20 with 1:38 left, but Shepard threw four straight incompletions.
Alex Thompson had seven catches for 109 yards and a touchdown for Northern Colorado, which had lost five of its last six. Harris finished with 57 yards rushing.
Northern Colorado took a 7-0 lead when Waggener hit Thompson with a 53-yard touchdown pass midway through the first quarter. After taking over on downs at their own 22, the Bears drove down and scored on Jace Davis' 24-yard touchdown reception early in the second quarter.
The Coyotes, who have lost four straight, then started their comeback. Shepard hit Tom Flanagan with an 8-yard touchdown pass with 1:01 left in the first half, then scored on a keeper from the 1 with 9:40 left in the third quarter to give South Dakota a 17-14 lead.
Shepard was 23 of 40 for 212 yards and two interceptions, and he ran for 46 yards. Chris Ganious led the Coyotes with 68 yards rushing.
