Rooney suffered a shin injury after clashing with team-mate Danny Welbeck in training and was unable to feature in the 1-1 draw at the DonBass Arena.
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"My plan wasn’t to use Wayne Rooney," the 50-year-old told reporters. "He picked up a crack on the shin and its swollen up. He was going to be on the bench but he has not been able to make it.
"I think he will be okay for Saturday. We could have risked him but we decided not to."
United’s 1-1 draw means they remain unbeaten in Group A after two games, yet Moyes suggests an air of disappointment lingers within the dressing room after the Red Devils went ahead in the first half and looked close to holding on for victory.
"We had to be harder to play against than we have in recent games and we were," the United manager continued.
"I’m beginning to understand the players a bit better. They were aware of how tough a game it was going to be and I thought we defended very well.
"There’s a bit of disappointment that we didn’t see the game out but I felt Shakhtar deserved something from the game."