United's assistant manager, Mike Phelan, insisted the decision was "tactical".
"Big decisions have to be made," he said. "The manager made those calls and we had the balance just right."
In the aftermath of the game, much of the attention in the British media has focused on Rooney's future.
The Times reported on Thursday that "Manchester United are willing to sell Wayne Rooney in the summer", while the Daily Mail claimed the striker was facing "a desperate fight" to save his Old Trafford career.
The speculation marks a complete turnaround from the events of October 2010, when Rooney accused the club of lacking ambition and was only persuaded to stay by a lucrative new five-year contract.
Since signing from Everton as a prodigiously gifted teenager in 2004, Rooney has enjoyed a glorious United career, winning four Premier League titles, two League Cups and the 2008 Champions League.
Though only 27, his 195 goals for the club put him in fourth place in United's all-time scoring chart, trailing only Bobby Charlton, Denis Law and Jack Rowley.
It had been assumed that Rooney would see out his playing career at Old Trafford, but although he remains a focal point for the English national team, Ferguson is reported to harbour concerns about his fitness and attitude.
The Scot has shown a ruthless lack of sentiment in the past, with Roy Keane, David Beckham, Ruud van Nistelrooy and Jaap Stam among the former United stars able to testify to the speed at which his opinion of a player can change.
However, as former United team-mate Michael Owen has acknowledged, if Rooney does elect to leave, there are not many clubs with a big enough budget and profile to attract a player of his status.
"Sometimes when you're at the level he is at, you don't have many options," Owen told British radio station talkSPORT.
"If you are a mediocre player, you have 20 teams in England and aboard that you can move to.
"If Wayne Rooney moves, where does he go to? Real Madrid, Barcelona, Bayern Munich, Manchester City, Chelsea and PSG - there's only half a dozen teams."
-AAP