Junior goalie Jessie Vetter (Cottage Grove, Wis.) made 20 saves as the Badgers finished their season with a 29-9-3 record.
On the other end, Kim Martin turned aside 28 shots for Minnesota Duluth (34-4-1), which won its fourth national championship and first since 2003.
UMD jumped out to a 1-0 lead on a controversial goal in the final minute of the opening period. Haley Irwin found a loose puck in front of the UW net and flipped it past Vetter during a delayed penalty, however a whistle was heard around the same time as when the puck went into the net. Following a review of the play, the goal was allowed to stand and the Bulldogs took a 1-0 lead into the first intermission.
The Bulldogs once again capitalized on a scramble in front of Vetter's crease midway through the second period. This time it was Emmanuelle Blais who pounced on the loose puck and extended the UMD lead to 2-0.
Sarah O'Toole increased the lead to 3-0 with a shorthanded goal late in the middle stanza. O'Toole intercepted a UW pass, skated in alone and beat Vetter for her ninth goal of the season.
Minnesota Duluth went on to add an empty-netter in the final three minutes as head coach Mark Johnson pulled Vetter for an extra attacker in the final minutes.
Wisconsin finished the game 0-for-10 on the power play while UMD went 1-for-6.
Junior Erika Lawler (Fitchburg, Mass.) was Wisconsin's lone representative on the Frozen Four All-Tournament Team. Lawler had a goal and an assist in Duluth, both during Thursday's 4-1 semifinal win over Harvard.