Wisconsin freshman goaltender Joel Rumpel was on top of his game in the opening 20 minutes, stopping all 15 shots that came his way, including four quality Minnesota opportunities on the power play.
As was the case on Friday, the Badgers opened the scoring in the series finale.
With senior Jake Hansen serving a two-minute minor for interference, Wisconsin's Tyler Barnes got the first goal of the game for the second night in a row.
Barnes whacked home a loose puck in front of Minnesota netminder Kent Patterson for his tenth goal of the season after a Mark Zengerle point shot was blocked in front.
Before the end of the middle frame, the game began to heat up after Gopher freshman Kyle Rau made a booming, open-ice hit on the Badgers' Joseph LaBate.
The Gophers staged a furious rally in the third period, scoring two goals before Wisconsin recorded its first shot on goal of the frame at the 11:18 mark.
The first of the two Minnesota goals came shorthanded after three players from each team were sent off 3:33 in. Sophomore Nick Bjugstad picked up the extra call on the play that began with the sophomore center driving hard to the net.
While killing off the ensuing Badger power play, Erik Haula seized a Badger turnover in the neutral zone and went in on a two-on-one with Hansen. Haula kept the puck and scored a highlight reel goal, cutting across the crease with his forehand and finishing the play with a top-shelf shot on the backhand.
Just over two minutes after Haula evened the score, Rau drew an interference call on Wisconsin captain John Ramage deep in the offensive zone.
On the Gopher power-play that followed, defenseman Nate Schmidt made a successful last-ditch effort to save a Badger clearing attempt from leaving the zone. After collecting the puck, Schmidt deked around a diving Wisconsin defender an unleashed a blistering slapshot into the rafters of the net to put the Gophers ahead with 12:20 to play.
The Badgers pulled Rumpel with 1:19 to play for an extra attacker, but couldn't muster a tying goal in the game's waning moments.
Patterson made five of his 17 saves on the night in the closing 20 minutes to seal the win.
With the win, Minnesota won on its Senior Night for the fourth straight year and improved to 13-1-1 when playing Wisconsin in its final home game of the regular season. Minnesota went 13-1-0 in the WCHA on Saturdays, including a perfect 7-0-0 mark at home.
The conference postseason begins next Friday when the Gophers kick off a best-of-three series against Alaska-Anchorage at Mariucci Arena. Each game will begin at 7 p.m.