Minnesota committed 22 turnovers - including two to open the second half, when the Cardinal opened up a double-digit lead they held for the rest of the game.
The Golden Gophers started three freshmen, a sophomore and a junior because of injuries to two key seniors: Trevor Mbakwe and Ralph Sampson III.
"I learned that we have got some pretty good players,'' coach Tubby Smith said of their performance in the NIT before Thursday's final.
"We have them all coming back - that's the best thing I learned about our team,'' he added.
And Mbakwe, Minnesota's leading scorer, could be coming back, too, after being granted a sixth season of eligibility by the NCAA.
The final minutes turned into a celebration of 3-pointers and fast-break layups for third-seeded Stanford (26-11), players on the bench jumping up to cheer on nearly every possession.
Both teams got off to a hot start, but then the Cardinal turned up the defensive pressure, and when the Golden Gophers (23-15) had good looks, they couldn't make them. Sixth-seeded Minnesota missed 16 of its last 19 shots in the first half.
The Cardinal scored 12 straight points to go ahead 29-21 with 4 1/2 minutes left before the break. Aaron Bright had six points, including a four-point play, and an assist during the run, and Stanford drew three charges.
Bright finished with 15 points and six assists off the bench to earn most outstanding player honors.
"When he comes in, it gives us a big lift and it gives our kids confidence in what they can do,'' coach Johnny Dawkins said of Bright, Stanford's third-leading scorer.
In front of a sparse crowd at Madison Square Garden, the atmosphere on the court had some sizzle. Minnesota's Elliott Eliason and Stanford's Dwight Powell had to be separated after getting tangled up on a held ball late in the first half, and the two exchanged words again in the second. Powell was later called for a contact technical foul when the Gophers' Rodney Williams hit the floor face first after being whistled for fouling the Cardinal forward.
Williams stayed on the court for several minutes before walking off under his own power and returned to the game soon thereafter.
It was the fourth foul on Williams, who at that juncture had scored 12 of Minnesota's 30 points. Williams, who made the all-tournament team, finished with 12 to lead the Gophers.
Powell hit both of his free throws, and in a sign of how the game was going for the Golden Gophers, Andre Hollins, a 92.2-percent foul shooter, made only one of two, and Stanford led 47-31 with less than 12 minutes left. Hollins, a freshman, also made the all-tournament team. He had five turnovers and zero assists.
"That's just unacceptable for a point guard,'' he said.
The Golden Gophers hit just three of their 13 3-point attempts and allowed the Cardinal to shoot 57.1 percent in the second half.
"When you're missing shots like that, you get a little frustrated, or you pick up a foul like Rodney did,'' Smith said. "You're a little discouraged.''