The England striker has misfired from the spot 10 times in his Old Trafford career and the 71-year-old believes he has better options from 12 yards already in his squad
Ryan Giggs netted from the spot after three minutes in United's 4-1 FA Cup win over Fulham at the weekend, despite Rooney featuring from the start.
The former Wales international has started just 11 matches this season but was handed responsibility after the England striker missed his 10th penalty for the club in their third round replay with West Ham.
The manager told reporters after the match: "I think Ryan's probably one of our best penalty takers, to be honest.
"I think it's fair that with Wayne missing the penalties he has, it was time to give him a break.
"He'll come back to it, though, there's no question about that."