Striker Rooney blazed his latest effort over against West Ham last month, the second time this season he has failed from the spot.
Ferguson indicated he needed to make a change, and when United got another penalty against Fulham last weekend, it was Ryan Giggs who stepped up to put his side ahead.
But Rooney has revealed Robin van Persie, who did not start on Saturday, has now taken over as United's number one taker.
"To be honest it was my choice," Rooney told MUTV.
"It wasn't good enough. I went in to speak with the manager and said I'd spoken with Robin and told him he could take them.
"At a club like this, to miss two penalties like I did and not hit the target wasn't good enough."