Wisconsin (36-1-4) completed its season with a 26-game unbeaten streak. The Badgers' only loss was to Minnesota Duluth (24-11-4) in November.
"We are extremely excited to take the trophy back to Madtown," said head coach Mark Johnson, using the nickname for the university's home of Madison, Wis.
Bauer, from St. Catharines, Ont., was a runner-up for the Patty Kazmaier Award on Saturday after finishing third in the NCAA with 63 points.
Ottawa's Jasmine Giles and Americans Jinelle Zaugg and Erika Lawler also scored for Wisconsin.
Montreal's Emmanuelle Blais replied for Minnesota Duluth.
"They did what we asked the last couple of months, step up, step up, dig deeper," coach Shannon Miller said. "They got it done and that's what got us here. I couldn't be more proud." She said the team just ran out of gas in the final game.
Zaugg's power-play goal at 9:00 of the first period at Herb Brooks Arena gave Wisconsin the lead. The Badgers took control with three goals in the second period. Lawler scored at 7:24 and Bauer added her 29th of the season at 11:56.
Blais deflected a shot from Noemie Marin of St-Hyacinthe, Que., past Wisconsin goaltender Jessie Vetter on a power play at 14:23 to end the Badgers' shutout streak at 422:36. It was the first NCAA playoff goal that Vetter and the Badgers had allowed since a victory over Mercyhurst in a 2006 quarter-final.
Ten seconds later, Wisconsin responded with a goal by Giles on the rebound of a shot by Lawler.