Rooney has been absent for the past two games while Smalling missed the defeat against Galatasaray with a shoulder problem. Jonny Evans is still rated doubtful for the match against the struggling Londoners.
"Wayne Rooney is fit," said the boss. "He had tonsillitis but has been training all week, which is good. Jonny Evans will hopefully train today but I don't know if he will be available for tomorrow. Chris Smalling had a small shoulder injury on Tuesday night.
"I wanted to play Phil Jones anyway - at least the two of them are back because I thought Jones did very well in his first game back, which is really good news. Nani is not available yet, he's not fit yet. He's still got a little problem with his hamstring."
Sir Alex is focused on getting back to winning ways against the capital club, who are currently bottom of the table and surprisingly dispensed of Mark Hughes' services on Friday morning.
"Hopefully, we can get back on track tomorrow after the disappointment of last week," he stated.
"If you analyse things a little bit more closely, it’s probably a lesson to everyone that changing a team and bringing 11 new players in to the [Barclays] Premier League is not easy. But I am surprised they’ve only got four points. I didn’t expect them to immediately set a blazing trail or be up at the top of the league or anything like that with 11 new players to bed in. But they’ve only four points and of course that creates its own headlines."