The second baseman's go-ahead hit gave the Ducks a crucial victory in their race for the Pac-12 crown over the conference's premier arm.
For the second straight season Oregon hit Stanford's Mark Appel well enough to get a victory, tallying eight hits Friday and 10 last season. Appel threw the entire game, striking out nine batters in the loss.
Pinch hitter Steven Packard scored the winning run on the Payne hit, reaching first when shortstop Drew Jackson threw the ball into the dugout instead of the first baseman's mitt to open the ninth inning. Connor Hofmann laid down a bunt that was effective enough to beat the throw and Appel intentionally walked J.J. Altobelli to load the bases.
"Bases loaded with nobody out, that was probably going to be one of our better shots," Payne said.
Payne watched Brett Thomas strike out swinging but was careful not to do the same.
"The first two I was just trying to hit something to the outfield," Payne said, "with two strikes I was just trying to put something in play and get the barrel on something."
Both teams' scored runs in the third inning, before playing deadlocked baseball until Payne's hit. Stanford scored in the top off a Danny Diekroeger double to left field that brought Austin Slater to the plate. The Ducks matched the run with a Ryon Healy single that scored Payne.
Oregon's Tommy Thorpe gave up seven hits in the first four innings, before settling in to hold the Cardinal to just two over the next three.
"Even in this park, you're kind of walking on egg shells because of their big strong guys in the middle," Horton said.
Thorpe and the Ducks were fortunate not to allow a run in the second, when a hard hit ball off the bat of Justin Ringo appeared to get past the Duck infield, only to be knocked down by Payne who threw out Alex Blandino who was turning for home.
The win was the team's first Friday win over a ranked opponent, and Oregon will attempt win it's first series of the season over a ranked opponent on Saturday and Sunday.
"Big boys come back strong. They're going to come back strong," Horton said.