Rooney missed his 10th spot-kick for United when he was off target in the FA Cup third-round replay against West Ham 10 days ago.
Ferguson felt it was time for a change, so when Aaron Hughes handled in the second minute of the fourth-round clash with Fulham, Rooney was passed over in favour of Ryan Giggs, who duly sent United on their way to a 4-1 win.
With Robin van Persie not even on the pitch, Rooney has slipped well down the penalty-taking pecking order. However, Ferguson does not think the England man's spot-kick days are over.
"With Wayne missing the penalties he has, it was time to give him a break," said Ferguson. "But he will come back it.
"The one thing about Wayne is that it doesn't faze him if he misses one. He has a fantastic temperament."
Rooney got his name on the scoresheet anyway, blasting home in the second half after Anderson provided the through-ball.
He then sent Javier Hernandez through for the first of his two goals before Hughes netted a consolation for the visitors, who were comprehensively outplayed.