Rooney was absent with tonsillitis while De Gea was unable to appear at Carrow Road after having his wisdom teeth removed.
But midfielders Shinji Kagawa and Nani, along with defender Jonny Evans, were absent when the training session began.
The trio have been struggling with knee, hamstring and groin injuries respectively.
United manager Sir Alex Ferguson later revealed that Kagawa will be on the sidelines for a second month.
United face Turkish club Galatasaray on Tuesday in Group H of the Champions League having already qualified for the knock-out stages.