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 its 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.
Ferguson added, "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."