Ferguson: Rooney may be missing for weeks
Rooney, 25, who has started the season in outstanding form with nine goals, missed Saturday's match when United dropped their first points of the season but stayed top of the Premier League on goal difference from Manchester City.
Ferguson told reporters: "Rooney's is not a serious injury, but it was enough to keep him out today, and I think maybe for a few weeks."
If that's the case Rooney will miss United's Champions League match with Basel at Old Trafford on Tuesday and possibly England's Euro 2012 qualifier in Montenegro on October 7.
He could also miss United's upcoming league matches against Norwich City and Liverpool and possibly the Manchester derby against City on October 23 as well as the Champions League match against Otelul Galati of Romania on October 18.
Rooney was not the only United player suffering with defender Jonny Evans injuring a foot in the warm-up at Stoke while Mexico striker Javier Hernandez went off early in the game after suffering a dead leg in an early collision with Stoke defender Jonathan Woodgate.