Rooney suffered a small injury during the clash with Aalborg on Tuesday, but has been called up for England’s upcoming World Cup qualifiers.
England face Kazakhstan next Saturday.
Fergie told the Daily Star: “If they decide to play him in one game and left him out on Saturday – it’s not an issue with me.
“I have no problems with Rooney joining up with the England squad.
“The saving grace is that they should win both games comfortably, even if he isn’t fit in time for next Saturday.
“But that is Fabio’s call to make, when he assesses how Wayne’s progressed over the next few days.
“That rests with Fabio. He’s got two games and I’m sure England will win both games.
“And he can cope without Wayne in that situation.
“I don’t think this is the biggest test for England. They have got players who are more than capable of filling Wayne’s boots in these games.
“But that is Fabio’s call. He might want to play him next Saturday – and I’m sure he will be fit for that.”