The comments in question came when ESPN sideline reporter Erin Andrews asked Kelly about a heated exchange he was having with the officials.
Said Kelly: "I just want to know why they won't come talk to us, I think [Stanford coach] Jim [Harbaugh] and him [the referee] got friends. I don't know, I just want some explanation on some things."
The Pac-10 released a statement from commissioner Larry Scott explaining the reprimand.
"The Pac-10 has specific rules that prohibit our coaches from making public comments about officiating, and this prohibition specifically includes comments that create doubts about the credibility of the conference's officiating program," Scott said. "The conference expects each Pac-10 coach to adhere to our standards of conduct and to conduct himself or herself in a manner which will reflect credit on the institution and the conference."
Oregon, which moved up to No. 3 in the AP top 25 poll this week, won the game 52-31.
Ted Miller writes about the Pac-10 for ESPN.com.