Rooney picked up a knock in training on Tuesday but is expected to partner Carlos Tevez in attack with Berbatov ill.
The £30million Bulgarian striker has been unable to train since his arrival in Japan after contracting a virus.
United manager Sir Alex Ferguson said: "Berbatov is not well at the moment. Rooney was injured in training on Tuesday but we hope he will be fit."
Ferguson has revealed his plan to hand starts to Paul Scholes, Ryan Giggs, Gary Neville and Cristiano Ronaldo on Thursday, saying Scholes' experience would be "vital" in Yokohama.
Despite the effect this Japanese excursion will have on United's title chances, with their next league match is not until Boxing Day, Ferguson insists United are serious about becoming the first British side to win the Club World Cup.
"It's a big incentive to become world champions," he said.
"In 30 years' time you look back and say 'Manchester United - world champions' - to me that is what our club's about."