The seventh-seeded Golden Gophers got 27 points from Whalen and 20 points and 18 rebounds from Janel McCarville to oust the top-seeded Blue Devils 82-75 in the Mideast Regional final Tuesday night.
Minnesota had already bounced second-seeded Kansas State and third-seeded Boston College on its improbable run to the Final Four.
The Golden Gophers led most of the way and answered every Duke rally.
"Coach (Pam) Borton said the most aggressive team was going to win and that's the way we've played all year," Whalen said. "Tonight we just got a few things to go for us and we just played loose and played together."
Duke (30-4) was turned away in its last bid to win a championship for All-American Alana Beard and fellow senior Iciss Tillis. Beard scored just 10 points on 4-for-14 shooting and was in tears as the game ended.
"You guys don't understand how it feels to go out there every single year thinking you're going to win the national championship and it doesn't go your way," Tillis said. "It hurts. It's really painful."
The Blue Devils had reached the Final Four the last two seasons, but lost in the semifinals both times.
"Going into the game I thought we were very ready to play, but early on I thought it appeared we were all pretty tight," Duke coach Gail Goestenkors said. "It's sometimes easier to be an underdog and just go out and play and understand that nobody expects you to win."
Minnesota (25-8) had never passed the round of 16 before this year. The Golden Gophers will go to New Orleans next week as the highest seed to play in a Final Four since Arkansas got that far as a ninth seed in 1998.
Whalen, McCarville and the Golden Gophers led most of the game, and by as many as 10, but didn't flinch when Monique Currie's layup with 5:33 left pulled the Blue Devils even at 59.
Working the ball around, the Gophers found Shannon Bolden in the left corner, and her third 3-pointer of the half pushed the lead back to three.
"They hit every big shot," Goestenkors said. "It seemed like every time we made a run and cut it to two or tied it, they'd come back and hit a huge three."
Duke answered with two free throws by Currie, but McCarville hit both ends of a one-and-one, drawing Tillis' fourth foul in the process.
Beard again pulled Duke within a point with a driving basket, her first field goal in 16 minutes and only fourth in the game, but the Gophers scored the next five points.
Kadidja Andersson hit a free throw, McCarville went around Tillis for a layup and then dropped a gorgeous pass behind her back to feed Whalen streaking to the basket for a layup.
Beard hit the second of two free throws for Duke, Currie hit a 12-footer and Lindsey Harding followed a free throw by McCarville to again pull Duke to 70-68 with 1:03 left.
Whalen scored and McCarville hit a free throw with 47.8 seconds left, making it 73-68.
Tillis' basket in the lane cut it to three with 37.3 seconds left, then Tillis fouled out four seconds later, putting Whalen at the line.
She made both and the Blue Devils never got closer than four again.
"This definitely has not sunk in yet," coach Pam Borton said.
Andersson added 17 points and Bolden 10 for Minnesota.
Currie led Duke with 19 points and Tillis had 12.
The Gophers led 42-32 in the second half when Tillis and Duke finally started clicking. Tillis hit two free throws and a layup, Brittany Hunter hit a baseline jumper and Tillis added a bank, the 8-0 run making it a two-point game.
But Minnesota was undaunted. Whalen hit McCarville with a no-look pass for a layup, Andersson scored in the lane and Whalen fed Andersson through traffic for another layup, making it 50-44.
The Blue Devils again pulled within one at 50-49, but Minnesota scored seven straight before Duke scored six in a row to get within 57-55.
The Golden Gophers led 33-26 at halftime, but 13 turnovers kept them from pulling away.