The Red Devils fly out to Spain on Tuesday morning for Wednesday's clash with the Primera Division leaders.
But the club confirmed on their website that England striker Rooney will not be among the travelling party after the 24-year-old was substituted in the second half of Sunday's draw with Bolton due to an ankle injury.
There has been no indication whether Rooney's absence will be any longer, which would threaten his participation in Saturday's Premier League encounter with Sunderland at the Stadium of Light, plus England's Euro 2012 qualifier with Montenegro on October 12.
While Ferguson's assistant Mike Phelan revealed Rooney is still struggling with a niggling ankle injury, some may feel it is a good time for Rooney to have a break.
On ESPN on Sunday, Kevin Keegan voiced his concern for the striker, who has scored only one goal for United this season, and that came from the penalty spot.
Although the furore over his private life has hardly helped, Rooney was so ineffective against Bolton that purely on form grounds Ferguson might have looked at a combination of Dimitar Berbatov and Michael Owen against Valencia anyway.
Now Rooney can have a couple of days away from the glare of publicity and try to get himself into the right frame of mind for when he next plays.