Sir Alex Ferguson revealed the striker will be assessed on Sunday after sustaining an ankle injury, while Theo Walcott is also a doubt for Wednesday's tie.
Rooney was substituted after 79 minutes during his side's win at Villa Park, and Manchester United boss Sir Alex Ferguson admits full extent of the injury has not yet been established.
"He's got an ankle knock and has ice on it. We'll see how he is tomorrow," Ferguson told Sky Sports.
Theo Walcott is also doubt for England's clash in Sweden after being brought off in the 85th minute during Arsenal's 3-3 draw at home to Fulham on Saturday.
"Walcott has a glute muscle problem. We nearly took him off at half-time, he nearly went down, but we left him on and on," Arsenal manager Arsene Wenger told reporters. "In the end, it got worse and worse. He is limping, so I do not know whether he will be able to join the national team or not."