Despite a spectacular performance from Stanford freshman goalkeeper Emily Oliver, Notre Dame got all it needed on a 63rd minute goal by Adriana Leon.
Stanford (23-1-2) went undefeated through the semifinals for the second consecutive season, only to lose in each final by a 1-0 score.
"It's a disappointing way to end the season," Stanford coach Paul Ratcliffe said. "I'm proud of the team. I thought they played well."
No Cardinal played better than Oliver, who made four spectacular saves in the second half to keep the match close.
Stanford's best chance came from an unlikely source, central defender Courtney Verloo, who hadn't scored all season. Verloo was given space and took it, carrying to within 20 yards of the goal, where she released a right-footed shot that hit the left post in the 17th minute.
In retrospect, the near-miss would prove to be big.
"If the shot from Courtney would have went in, I think that would have broken the ice for us and boosted our confidence, and we could have won today," Ratcliffe said.
Notre Dame (21-2-2) became the first school other than North Carolina to win at least three titles. The Irish took the lead when Melissa Henderson beat two defenders to the end line before slotted a pass across the goal to an onrushing Leon, whose 10-yard shot traveled over the right shoulder of Oliver.
It marked the first time since Sept. 10, and only the third time all season that Stanford had trailed.
With Stanford pushing forward for the equalizer, its defense often was left vulnerable, leaving Oliver to deal with several harrowing situations
But, other than a far post header by Alina Garciamendez on Lindsay Taylor's free kick that was saved, Stanford was unable to mount a dangerous threat the rest of the way.
"It's really bitter," said Christen Press, the nation's leading scorer who was limited to three shots. "We worked so hard for it. But at the end of the day, soccer is a crazy game, and I've learned over the years that's how it goes."
The match began under partly cloudy skies, but with a temperature of 37 degrees, with gusts of 20 mph contributing to a 31-degree wind chill. A Saturday snowstorm forced the field to be watered and plowed, clearing it before kickoff.
Before a crowd of 7,833, Stanford didn't take long to control much of the possession, and was able to push regularly into the Notre Dame half. However, Notre Dame captain Jessica Schuveiller was able to contain Press, who was unable to turn into space and get the opening she needed to unleash a shot.
After that Notre Dame began to establish its offensive attack. Stanford's outside back Rachel Quon blocked a dangerous cross as she tracked back to the goal, and the Irish had an even better opportunity when Henderson's near-post header off a cross was saved by diving goalkeeper Oliver, who deflected the ball into the crossbar.
As the half drew to a close, Notre Dame's Rose Augustin partially got a foot on a cross that curled away from Oliver, and Garciamendez scrambled to clear it out.
Notre Dame did not allow Stanford's outside backs, Quon and Annie Case, to get forward, dropping its wingers to absorb potential attacks. By funneling the offense into the middle, Stanford had little room to maneuver.
Stanford wasn't helped by having to play against the wind in the second half. Though Taylor got off two quick shots to begin the half, the action began to go end to end.
Henderson shot barely wide at the far post for Notre Dame, and then Mariah Nogueira shot just high after a well-conceived dummy pass from Lindsay Taylor in the 57th minute.
Once Notre Dame scored, Stanford extended itself in an effort to tie the score, but the Irish took advantage with counterattacks that put Oliver to the test.
She denied Henderson by pushing her shot high. Later, she saved a point-blank shot by Leon, and then saved Henderson cross-goal shot with her right hand.
Another point-blank attempt by Leon was stopped by Oliver's left hand.
"I didn't know she was a freshman until today," Henderson said. "I think she's absolutely tremendous. She made so many great saves and I have so much respect for her and everything she did today."
The match marked the end of the collegiate careers of Press -- who finished tied with Kelley O'Hara (2009) for Stanford's single-season goal-scoring record - as well as captain Allison McCann, Kira Maker, and Morgan Redman.
The Cardinal will return nine starters and four All-Americans - Nogueira, Taylor, Verloo, and Teresa Noyola. Now, the challenge will be to continue its success and exceed it, with another quest toward an NCAA championship.
"It's been a lot of fun playing for Stanford," said Press, who will graduate with every Stanford career scoring record. "It's a great team and a great program. Performances like Emily's today just inspire you. They have a great future ahead."
All-Tournament team
Most Outstanding Player on Defense: Jessica Schuveiller (Notre Dame)
Most Outstanding Player on Offense: Melissa Henderson (Notre Dame)
Stanford: Camille Levin, F; Emily Oliver, GK; Christen Press, F. Notre Dame: Rose Augustin, F; Courtney Barg, M; Melissa Henderson, F; Mandy Laddish, M; Adriana Leon, F; Jessica Schuveiller, D. Boston College: Hannah Cerrone, D. Ohio State: Katie Baumgardner, GK.
-- David Kiefer, Stanford Athletics