The forward will almost certainly miss Manchester United's visit to Blackburn on Saturday with an ankle injury but Ferguson has played down fears he could fail to join Capello's squad for the qualifiers at home to Kazakhstan on 11 October and away to Belarus four days later.
Rooney limped out of United's impressive UEFA Champions League win over Aalborg in Denmark this week, generating concern that he would be unavailable for the England games.
But, although Ferguson is unable to guarantee his fitness for the first of the matches, the United manager has assured England boss Capello that Rooney will be joining the squad.
"I have no issue about Wayne Rooney joining England," said Ferguson, who rated Rooney "doubtful" for the visit to Blackburn, now managed by former United star Paul Ince. "The only saving grace about him is that the games England have, they should be able to cope even if Wayne wasn't to make the Saturday game."
While Rooney is making a positive recovery from his injury, midfielder Paul Scholes has been ruled out for ten weeks after damaging knee ligaments in the same game this week.
However, despite Scholes approaching his 34th birthday and being in the final year of his current Old Trafford contract, Ferguson has no doubt the influential veteran will make a full and impressive return to first team action.
"The last few years, Paul has had some longer term injuries like this," said Ferguson. "But he has always come back nice and fresh. "Of course, he is 34 next month but he is like Ryan Giggs and Gary Neville in how he looks after himself.
"He is only a couple of months apart from Gary in age and Gary has just been out a year and a half, but he has come back absolutely fantastically. You have got to admire that perseverance and determination, it's an in-bred characteristic they have.
"They look after themselves and that's the reason I am very very confident Paul will be back and playing, easily for another year. I have no fears about that, he has come back repeatedly.
"The problem Paul had with his eye was a worry at the time a couple of years ago because we couldn't find the answer to it. We were worried about that. But he came back from that and came back from injury last season. He'll come back from injury this year."
United's faith in Scholes was underlined on Friday when the midfielder signed an extension to his contract which will keep him on the Old Trafford payroll until the end of next season.
Darren Fletcher has also been given a new deal with his contract now extended to 2012.
Ferguson's claims that he has a deep squad are currently being put to the test with key midfielders Michael Carrick and Owen Hargreaves sidelined and Neville, like Rooney, rated doubtful to play at Blackburn.
But Ferguson is content with the way in which his personnel have responded to the number of absentees.
"I think we will continue to get better," he said. "We have players now getting more miles on the clock and who are now getting games and we're strong. Very strong.
"You see the value of the squad now when you see the players we have out. At the moment we have three midfielders out but then you see the way John O'Shea played in midfield on Tuesday, he was excellent. Players like Anderson, Giggs, Fletcher have come in and done well. I'm blessed with a strong squad and we should cope."