Rooney was substituted half-an-hour from the end of the 2-2 draw with Bolton at the Reebok Stadium and Phelan confirmed afterwards the United striker was still being troubled by a niggling ankle injury.
That might explain why Rooney was so ineffective, and why he still has not scored a goal in open play for the Red Devils this season.
"Wayne Rooney had a bit of a knock," said Phelan. "He has a little issue with his ankle. We don't know how serious.
"We will have a look in the morning but we think he will be OK for Wednesday.
"He has been playing with it for a couple of weeks now and during the game we decided he wasn't getting into the areas we wanted and he wasn't getting chances, so we had to change it."
One man who apparently will miss out on the flight to Spain is Ryan Giggs, with Sir Alex Ferguson confirming the veteran wideman will be out for two weeks after a suffering a slight hamstring strain.
"Ryan is the most serious," Ferguson told ESPN.
"It is a hamstring and I am afraid he will be out for a couple of weeks."
Ferguson also decided to rest Rio Ferdinand in preparation for the Valencia encounter and again saw his side concede sloppy goals.
Twice they went behind, through Zat Knight early in the contest and Martin Petrov in the second half at a time when the Red Devils were looking to take control.
Although United rallied through Nani and Michael Owen, whose third goal in a week puts Rooney's problems in front of goal into sharp focus, they were unable to take full advantage of defeats for Chelsea and Arsenal yesterday.
"In the first half we should have done better but we did well to come from behind," said Ferguson. "The second half was very even. Bolton were a real handful and our chances were reduced but we must take credit for coming back again. It shows a bit of character."
Ferguson must now decide whether to stick with Rooney or partner Owen with Berbatov after the former Liverpool star flicked Nani's near-post free-kick into the far corner 16 minutes from time.
"Scoring goals has always been part of my career, but this one is tinged with a bit of disappointment at not getting three points," said Owen.
"Were helped with a few nice results yesterday but when you don't capitalise fully it is disappointing. It is a long season and we will bounce back."
As Bolton manager Owen Coyle had claimed this would be an accurate guide of his side's progress considering they lost the corresponding fixture last season by four goals, the Scot was satisfied with his side's efforts, if slightly frustrated by the outcome.
"Having lead twice, we were disappointed to give up those leads, but you have to give balance to the unbelievable individual quality they have," he said
Coyle was left to reflect on the golden opportunity Johan Elmander spurned before Owen struck, which surely would have sealed the Trotters' victory.
"That chance would never have happened if Johan hadn't taken the ball, driven 40 yards and beat three or four men," said Coyle.
"He was magnificent. He is a player playing at the top of his confidence.
"On another day that ball would have rolled into the top corner.
"I am certainly not going to criticise a player who's given me everything and shown unbelievable quality as well."
Coyle also had words of encouragement for Rooney, who was making his first appearance away from Old Trafford since the storm over his private life erupted.
"Wayne Rooney as a footballer is an absolutely class act," he said.
"I have always felt Manchester United and England as a country are very fortunate to have him."