Mastodon senior forward Frank Gaines scored a game-high 22 points, while Joe Edwards added 11.
Michael Kibiloski and Pierre Bland each scored eight, Bland's representing a new career-high.
Mario Hines pulled down a game-high seven rebounds, as IPFW outrebounded the Coyotes 36-to-29, while Isaiah McCray dished out four assists.
With the weekend sweep (IPFW topped Kansas City on Thursday), IPFW improves to 12-16 on the season and 5-9 in Summit League play, into sole possession of sixth place in the league standings, and in position for the fifth seed in for the 2013 Summit League Tournament.
South Dakota falls to 8-18 overall and 4-10 in the league, and into a two-way tie for eighth place in the league standings.
IPFW jumped out quickly, scoring first 36 seconds into the game, and never trailing for the remaining 39:24.
South Dakota twice climbed to within two, the final time with 11:42 to play in the opening half, before IPFW scored five straight on a three-pointer by Gaines and a lay-in by Eddwards.
The Mastodon lead reached double figures at 12 to cap a 6-0 IPFW run, and the Dons closed the first half on a 9-0 run, forcing the Coyotes into three turnovers in their final four possessions of the first half to take a 36-17 lead into the locker room at halftime.
South Dakota opened the second half on an 8-2 run to climb to within 11, but could not drop the deficit to single digits, as IPFW led by as many as 21 in the second half, cruising to the 13-point victory.
IPFW hit 27-of-61 shots from the field (44.3 percent), 7-of-23 from long range (30.4 percent), and half of their six free throw tries.
South Dakota went 19-of-50 from the field (38.0 percent), 5-of-17 from beyond the arc (29.4 percent), and 57.1 percent (8-of-14) free throws.
The Coyotes were led by Trevor Guis who scored 12 points, eight of those coming in the second half, while Casey Kasperbauer scored 11, and Juevol Myles 10.
The Mastodons will host Oakland Wednesday at 7 p.m. at the Memorial Coliseum.