The Cardinal had the nation's best run defense going into the game, allowing an average of just 54.8 yards a game. Oregon, meanwhile, had the country's third-best rushing offense, averaging 325 yards a game.
Stanford held Ducks running back Kenjon Barner, who was averaging 136 yards rushing a game, to just 66 yards. Overall, the Ducks managed only 198 yards on the ground.
Oregon's top rusher was Mariota, who ran for 89 yards. The redshirt freshman who had been getting Heisman buzz, threw for 207 yards and a touchdown.
Stanford stuffed what appeared to be a sure first-quarter Oregon touchdown drive when Mariota took off on a 77-yard keeper to the Stanford 15. But the Ducks couldn't get much closer, and Stanford got the stop when Oregon went for it on fourth-and-2 on the Cardinal 7.
Stanford scored first on Hogan's 1-yard plow into the end zone early in the second quarter, but Oregon answered with Mariota's 28-yard touchdown pass to Keanon Lowe to tie it at 7-all.
Oregon extended its lead to 14-7 on De'Anthony Thomas' 6-yard scoring run in the third quarter, but missed a chance when Maldonado's 42-yard field goal attempt went wide right.
Williamson missed a 43-yard field goal attempt for Stanford early in the fourth quarter.
The Ducks went into the game hurting on defense after a 59-17 victory over California last weekend.
Oregon was without free safety Avery Patterson seriously injured his left knee in the second quarter and is believed to be out for the rest of the season. Patterson had taken over as starter for senior John Boyett, whose career at Oregon ended earlier this season when he needed surgery on both knees. Starting nose guard Wade Keliikipi did not play.
Because the Ducks do not disclose injuries, there was also uncertainty about the secondary, leading to speculation that the team might use Lowe or even multi-purpose sophomore back Thomas on defense. But they did not.
"One thing we take pride in is we don't make excuses," Kelly said. "The No. 1 stuff and the injury stuff everybody else has to deal with, so we don't make excuses. Stanford played better than us tonight and they won the football game."
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