Stanford added two field goals in the second quarter to take a 16-6 lead over Notre Dame into the break.
A big defensive play kept Notre Dame out of too big of a hole going into halftime.
Irish safety Jamoris Slaughter picked off a pass by Stanford quarterback Andrew Luck after cornerback Robert Blanton tipped the ball to keep the Cardinal's lead at 13-6 entering the break.
Slaughter returned the pick to the 28-yard line with 1:21 to play, but the Irish started their last drive of the half at their 14 after Manti Te'o was called for clipping during the interception return.
But the Irish gave the ball right back after three ineffective offensive plays, and the Cardinal got a 36-yard field goal from Nate Whitaker with four seconds left.
Notre Dame's defense is getting burned on third downs. Stanford has converted 7 of 9 third-down attempts.
Even though the Irish have only given up field goals after the Cardinal's first-quarter touchdown, they have to find away to force three-and-outs in the second half to have a chance.
Notre Dame pulled within four at the start of the second quarter.
Kicker David Ruffer hit a 40-yard field goal to cut the Irish's deficit to 10-6 with 13:22 to play in the second quarter. Ruffer capped a 61-yard, 12-play drive that spanned the first and second quarters.
Stanford answered with a field goal of its own with 4:59 to play in the first half when Whitaker hit a 41-yarder.
Notre Dame's defense was getting torched on third downs, until the Irish finally came up with a stop at third-and-13 from the 23-yard line. Stanford went 3 of 4 on third downs on the drive.
Luck has been as good as advertised completing 15 of 23 passes for 176 yards and making a number of tight throws. He has also gotten help from a running game that has produced 61 yards.
Notre Dame's running game wasn't able to get going in the first half, gaining 24 yards. Dayne Crist has had trouble getting going offensively, throwing for 96 yards and being sacked twice in the first half.