While City push for the title, United's very slim hopes of a top-four finish must now been gone.
Rooney acknowledged United did not do enough to take anything from the game.
"It's a bad night and we didn't deserve to win," the United striker said. "We weren't clinical enough and we didn't create enough chances.
"No-one likes to lose a derby game - they're big games and they're great to win, but when you lose it's not a great feeling.
"It's probably been the story of our season so far that we've got a couple of good results and then one which sets us back a bit."
Rooney added: "It's a bad night for us all but we have to move on.
"We've got two big games coming up against Bayern Munich but first we have to focus on the Villa game and try to end the season on a positive note."
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