James had 25 carries for 136 yards and caught two passes for 87 yards for the Ducks (6-0), 3-0 Pac-10), who have posted their first 6-0 start since 2002.
Darron Thomas completed 8-of-12 passes for 153 yards and a score, but was taken out of the game with an undisclosed injury. He was replaced by Nate Costa, who went 13-for-15 for 151 yards and a touchdown in relief.
Jeff Maehl hauled down 10 catches for 119 yards and a score for the victors.
The Cougars (1-5, 0-3) were led by Jeff Tuel, who went 25-of-40 passing for 245 yards and a touchdown.
Ten of the completions went to Jared Karstetter, who racked up 106 yards receiving.
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