The United striker limped out of the action 13 minutes from the end of this afternoon's 4-0 win over Stoke, sparking immediate fears about his health ahead of Fabio Capello's provisional squad being announced on Tuesday.
But, in confirming Rooney had aggravated a groin injury that first surfaced at Blackburn last month, Ferguson stressed he was not too concerned about the 24-year-old.
"He has aggravated his groin again," said Ferguson. "I don't think it is serious. I think he will be OK for England."
Capello will hope Ferguson's reassuring words prove to be accurate as the Italian can hardly afford to lose his talisman at this stage.
Under the circumstances, even if he is willing to play, Capello might not want to risk Rooney on the difficult Wembley surface when England tackle Mexico on May 24.
That would give him three weeks to get fit for the final friendly against Japan in Austria, and then almost two more before England open their Group C campaign against the United States in Rustenburg on June 12.
It was the most disappointing moment on a downbeat day when United managed to score four times, despite the knowledge the title was heading for Chelsea after a three-year stay at Old Trafford.
Darren Fletcher and Ryan Giggs put the hosts in the comfort zone before the break, although by then, Ferguson already knew United's fate.
"It was always going to be hard for Wigan to get something," said Ferguson.
"When we heard they were down to 10 men all our hopes evaporated.
"I am not going to agonise about where it went wrong.
"You could talk about a lot of things and the decision at Stamford Bridge was a bad one that turned the whole thing round.
"But you can't agonise over these things. Sometimes you get the breaks, on other occasions you don't.
"The European Cup was the biggest disappointment. We should be in the final.
"But we applaud Chelsea winning the title and I applaud Carlo Ancelotti. We know how hard it is to win the league."
Rooney has already identified one area where United need to strengthen, attack. And Ferguson hinted there may be new faces on the way.
"We are looking at the structure of the club," he said.
"There may be one or two things but at the moment nothing is signed."
As he addressed United's supporters - many of whom were wearing the anti-Glazer green and gold and made their feelings known both outside the ground before the game and inside it at the start and end of the second-half by blowing their whistles - Ferguson assured them United would be fighting back next term.
"We can be proud," he said. "We have challenged very strongly for a fourth title in a row and we have taken it to the wire.
"But next season we will go again and hopefully we will bring back the title to the best place in the world."