The 30-year-old recently attracted severe criticism for his below-par performance in the 3-1 defeat to Watford and was subsequently dropped from the starting eleven for the game against Leicester City.
Rooney also started on the bench against Zorya Luhansk in the Europa League on Thursday night but Scholes expects his quality to return in time for more significant matches against top Premier League clubs.
Scholes told BT Sport: "I just think he is not in the greatest of form at the minute.
"And the timing is right for him not to be in the team.
"Wayne's a fighter. He won't sit back and just let this happen. He'll be fighting to get back into this team.
"I'm certain he'll be back [for those games]."