Whalen scored 16 points on 6-for-13 shooting, but the swarming Purdue defense forced her into nine turnovers.
Meanwhile, the No. 9 Boilermakers (14-2, 4-1 Big Ten) outrebounded Minnesota 38-29 and hit 34 of 41 free throws, compared to 7 of 12 for the Gophers (15-1, 4-1).
Junior center Janel McCarville led Minnesota with 18 points and nine rebounds, but she was one of three Gophers -- along with forwards Shannon Bolden and Kadidja Andersson -- to foul out.
On Thursday, Minnesota's three freshmen came off the bench to outscore Illinois' reserves 24-11. But on Sunday, Liz Podominick, Jamie Broback and Kelly Roysland were held scoreless in a combined 41 minutes of action, missing all nine shots they took.
Sophomore point guard Shannon Schonrock provided one bright spot for Minnesota, overcoming a recent shooting slump to hit four 3-pointers on the day.
Purdue was led by all-America candidate Shereka Wright. She scored half of her 24 points from the free-throw line and grabbed a game-high 10 boards.
The Gophers shot a dreadful 29.6 percent from the floor in the first half and fell behind 17-6 in the early going. And even though they rallied to take a 23-22 lead, they gave up a 10-0 Purdue run to end the half.
Minnesota bounced back in the second half, shooting 56 percent from the floor, and cut Purdue's lead to 53-50 on a Schonrock 3-pointer, but down the stretch the Gophers' shots didn't fall and the Boilermakers hit their free throws.
In fact, Purdue shot just 32.6 percent from the field on Sunday, but scored more than half its points from the charity stripe as the Gophers were whistled for 27 fouls to just 18 for the home team.
Minnesota's tough road swing continues Thursday with a game at No. 8 Penn State.
Boilermakers derail Whalen, Gophers
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