Moyes said he was going to leave Rooney among the substitutes despite his recent impressive form.
But the England forward was not even named on the bench for the clash at the Donbass Arena, although he did make the short journey from the team hotel to watch the match.
"My plan wasn't to use him anyway, but he's got an injury," Moyes told Sky Sports.
"He picked up a crack to the shin yesterday [Tuesday] in training so that's made the job easy."
It is Rooney's fourth injury absence this season already.
The 27-year-old suffered a hamstring injury that effectively ruled him out of United's pre-season tour to the Far East and Australia.
Then he was sidelined from the remainder of United's pre-season campaign with a shoulder injury, before suffering a nasty gash on the head in an accidental training ground incident with Phil Jones that saw him miss the defeat at Liverpool and two England World Cup qualifiers.
Three Lions boss Roy Hodgson will be crossing his fingers that Rooney's absence this time around does not rob him of his talisman for the crucial World Cup qualifiers against Montenegro and Poland at Wembley over the next fortnight.