Kelly made the comments while doing an interview with ESPN's Erin Andrews.
Andrews asked Kelly what he was "barking" at the officials during the closing moments of the half.
"I just want to know why they won't come talk to us, I think (Stanford coach) Jim (Harbaugh) and him (the head referee) got friends. I don't know I just want some explanation on some things," Kelly said.
Oregon went on to win 52-31. The Ducks are the third-ranked team in the nation this week.
Pac-10 commissioner Larry Scott issued the statement of 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."