Ryan Giggs got the job at Old Trafford on Sunday after Rooney had missed his tenth penalty against West Ham United in the previous round.
Ferguson decided that Giggs should be the man for the job on a temporary basis in the absence of Robin van Persie and it took just four minutes of the tie with Fulham before he had his chance and converted the kick to put United on their way to a 4-1 win.
But it's not all over for Rooney as the United boss confirmed to reporters after the game: "With Wayne missing the penalties he has, it was time to give him a break.
"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."