Sophomore Dustin Little (Castlewood) nailed a three-pointer from the top of the key with 5.2 seconds left in regulation to send the Coyotes and the Warriors into overtime after WSU's shot fell short at the buzzer.
However, in overtime, WSU's leading scorer David Zellmann, who was 2-of-10 from three-point range in regulation, hit a three-pointer at the 4:33 mark of overtime to put the Warriors ahead, 66-63.
Winona State's Quincy Henderson then scored a lay-up 11 seconds later to put the Warriors ahead by five points, 68-63.
The Coyotes, who played the overtime having four players with four fouls, countered the Warriors scores for the next two possessions, but after Winona State scored the following three-points on free throws, the last with one minute left, USD was unable to recover.
In the overtime session, WSU hit 8-of-9 free throws to seal the game.
In the first half, USD trailed until the 9:15 mark when freshman Mitch Begeman (Sioux Falls) hit a three-pointer from the left wing to put the Coyotes ahead for the first time, 19-18.
Two straight three-point plays by senior All-American Turner Trofholz (Schuyler, NE) sandwiched a Henderson three-pointer to give USD 29-28 lead at 3:21. Trofholz scored 15 points in the first half. The Coyote lead was then extended five points, 34-29, with 52 seconds left in the half on a pair of Trofholz free throws.
Zellmann then hit a three-pointer with 27 seconds left in the half to cut the margin to 34-32 at intermission.
The Warriors scored the first five points of the second half before USD went on a 7-2 run to take a five-point lead, 44-39. The run was fueled by three three-pointers, including two from Begeman, who finished with 12 points to tie his career-high (Morningside; Dec. 5, 2005).
USD held five-point leads twice more in the half with the last coming at 2:35 on a pair of free throws by redshirt freshman Jesse Becker (Plymouth, MN) to make the score 58-53.
The Coyotes had a chance to close out the game, but Winona State's Jonte Flowers hit a three-pointer in the corner with 1:14 left to cut the USD lead to one, 60-59.
USD then turned the ball over twice in the final 50 seconds and the Warriors hit a field goal and a pair of free throws to set up Little's heroics.
"I had a great look at the basket and the defender had sagged off of me after (Jesse) Becker drove to the basket," said Little in the post-game press conference.
For the game, USD shot 31.9 percent (23-of-72) from the field, including 30 percent (9-of-30) from beyond the three-point arc. The Coyotes saving grace was that it hit 14-of-17 (82.4 percent) of its free throw attempts.
Trofholz, who was held scoreless in the second half, led USD with 21 points and 10 rebounds to finish with 1,931 career points (third, USD) and 917 career rebounds (second, USD). It was the 90th time in his career (65th straight) that Trofholz scored in double figures. The double double gave Trofholz 30 for his career, including 16 this season.
Becker finished with 13 points, while Little and senior David Nour (Armour) added 12 and 10, respectively.
Winona State shot 43.1 percent (28-of-65) from the field and 33.3 percent (8-of-24) from three-point range. At the line, the Warriors shot 60.7 percent (17-of-28), with nine attempts coming in the overtime period.
The Warriors' John Smith led all players with 24 points and 15 rebounds before fouling out. Zellmann finished with 19 points, while Henderson and Flowers added 15 and 10, respectively. Flowers also recorded a double double by adding 11 rebounds.
"Our seniors did a super job. All of our guys played great and really hustled," said USD head coach Dave Boots, who recorded his 12th 20-win season at South Dakota this season. "It was a great college basketball game; we just weren't able to come through in the overtime."