Rooney missed the second-half spot kick that would have all but sealed victory at Old Trafford. Even though United won 1-0, Keane believes that it would have been enough for Ferguson to hand penalty duties to Robin van Persie for future matches.
Keane told The Mirror: "[Ferguson] will be fuming. I think that will be the last penalty Rooney takes for United.
"He could have made things a lot easier. The last thing the manager would have wanted was for the game to go to extra-time.
"Wayne has missed 10 now and that is far too many. Clearly he is not up to it in terms of taking penalties. Van Persie I'm sure will be delighted to take over that role."
Despite the miss, Rooney did score the winning goal to earn Manchester United a FA Cup fourth-round tie against Fulham.