Rooney, who has designs on being United's next skipper, started the match at FedEx Field in Washington but for the third time on the club's pre-season tour of the US, he was overlooked.
New manager Van Gaal is yet to settle on his permanent captain, although fellow Dutchman Robin van Persie is being touted for the honour, given the relationship the pair have developed at national level.
Rooney, who has twice been on the verge of leaving Old Trafford, signed a new deal last season and looked set to become skipper with the club under the stewardship of David Moyes.
But with the sacking of Moyes and the subsequent arrival of Van Gaal, the dynamic has shifted.
Rooney, who has scored four times in United's first two tour matches, said after the Roma victory that he will accept any decision Van Gaal makes.
"Of course I would like the captaincy but it is the manager’s decision who he chooses," said Rooney. "I think he wants to work with the players and choose a captain from there. I don’t think he was ever going to walk in and choose a player from the off. I’m sure he will look at the players now and make his decision in a couple of weeks."
- Sports & Recreation
- Tom Cleverley
- Van Gaal