Rooney clashed with Bluebirds midfielder Jordon Mutch in the eighth minute at Cardiff City Stadium, kicking his opponent and appearing to strike him with his left arm as they began to tumble to the ground.
But referee Neil Swarbrick deemed a yellow card enough punishment, and Rooney went on to open the scoring with a turn and low finish, before his corner allowed Patrice Evra to head home United's second.
However, Cardiff twice levelled, with Fraizer Campbell finishing from a sumptuous Mutch pass against his former club, before Kim Bo-kyung headed in to earn a point in stoppage time.
Moyes felt Swarbrick had got the Rooney decision right, but believed his side had lost concentration when the referee pulled Gary Medel and Marouane Fellaini to one side, after the Chile midfielder appeared to slap the Belgian as Cardiff prepared to take the free-kick from which Kim scored.
Moyes said: "I think Mutch runs across his path and runs down the line of the ball and I think Wayne's half in motion, I don't think it is any more than a booking that's for sure."
Of the Medel incident, he added: "I think if the referee sees it, he must have stopped the game for something because, most importantly, we lost our concentration.
"They actually have delivered the first ball in, so Peter Whittingham has had the chance to cross one in as the referee is blowing up.
"So he has his sighter for the second one and I thought we lost concentration with it more than anything at that point.
"I don't know what the referee can do in that situation but I am sure he had seen something to call them out, and I just think it actually worked against us as we were set, and we didn't defend as well as we should have done on the next ball."