The Bears outrebounded Stanford, held Brook Lopez to two points in the first half—15 total—and got Robin Lopez into foul trouble.
"I'm sure glad we don't have to play them again," Stanford coach Trent Johnson said.
Cal cut its deficit to one point only once and to two points nine times in the 2nd half.
Cal lost 79-69, its 14th loss in the last 15 meetings at Stanford.
Every time the Bears (15-10, 6-8) cut the deficit down to two, as much as 16 points, a miscue was seemingly inevitable. There was a turnover by sophomore point guard Jerome Randle, a failed box-out, or a missed defensive assignment to fuel Stanford (22-4, 11-3).
Even Cal's shots failed to go in. The Bears, who lead the conference in scoring at 78.2 points a game, were limited to 69 on 47.2 percent shooting.
Midway through the second half, leading scorer Ryan Anderson missed two open three-point looks that would have given the Bears their first lead since 3-2.
Randle failed to even draw iron on a potential go-ahead long-range shot.
"When you play against the Lopez twins, you rush your shots a little bit," Cal coach Ben Braun said.
"It's hard to get a lot of looks when there is a seven-footer chasing you all over the court," Anderson said.
It was a disheartening loss, being that it was so close and would have boosted Cal's postseason hopes so much.
A road win against a top-10 team would have meant the world to the Bears, who remain on the NCAA Tournament bubble. They will most likely need to win three of their final four regular-season games, which include both a home date against nationally ranked Washington State and a road trip to Los Angeles.
If the postseason doesn't come calling, Cal will be left reminiscing the following missed opportunities at Stanford:
Brook Lopez picked up a foul on the Bears' first possession, but Cal didn't go at him again until the 14-minute mark, and he didn't commit another foul.
"It's a different game if we can get them into foul trouble," Braun said. "You've got to find ways to go hard to the basket. It's a mistake to say, 'Let's just settle for outside shots.' "
No Cal player made more than one three-pointer with Anderson, Christopher, and Randle combining to go 3-for-12. The Bears average 37.5 percent from three-point range but connected on only 25 percent.
Even with Anderson, who shot 2-for-13, struggling, the Bears were in it, but they couldn't find another offensive option. Sophomore wing Patrick Christopher needed 20 shots to score 15, and no one else was in double figures with Randle the closest, scoring nine on 3-for-9 shooting.
"We had a lot of opportunities on offense and came away without getting a foul (or a basket)," Braun said. "That's on us. I can tell you that it's not, but it was."
In some respects, the Bears' Jamal Boykin, Harper Kamp, and Jordan Wilkes outplayed Brook and Robin Lopez. The Cal reserve posts combined for 20 points on 9-for-11 shooting and nine rebounds, but Stanford guard Anthony Goods' 20 points cushioned the Lopez twin's combined 26 points and 13 rebounds.
Cal started terribly, allowing 11-0 and 12-2 runs, but managed to head into the break only down 33-29. Using a 13-0 run—9-0 without Anderson on the floor—the Bears cut the lead to 28-25, but couldn't build off that.