Ronaldo, 37, made his comeback against the Spanish side after missing United's tour of Thailand and Australia to deal with a family issue.
He started the game before being replaced after the first 45 minutes. He was pictured leaving Old Trafford before the final whistle, with United sources afterward refusing to comment on whether his early exit was sanctioned by manager Erik ten Hag.
Ronaldo is keen to leave the club this summer in a bid to find regular Champions League football elsewhere. He has been linked with moves to Bayern Munich, Chelsea and Atletico Madrid, although sources have told ESPN that United are yet to receive a serious offer for the Portugal forward.
Sources have told ESPN that Ten Hag encouraged the squad members who played against Atletico Madrid 24 hours earlier to attend the friendly against Rayo.
Marcus Rashford, Anthony Martial and Scott McTominay were among the players who watched from the directors' box while others were in hospitality boxes. They looked on as Ronaldo's replacement, Amad, opened the scoring for United early in the second half before Alvaro Garcia equalised for the visitors soon afterwards as United ended their preseason campaign with three wins, two draws and a defeat from their six games.
"Overall, I am happy, we made a good preseason," Ten Hag said. "We make good progress and we're ready for the season, but still I know there is a lot of room for improvement and we have to improve.
"It's also a process that continues during the season, but for next week it's about a result as well. The reception was fantastic. I felt the vibe in the stadium, I felt the vibe they want to send to the team.
"There has to be co-operation between fans and the team so we get the right emotion and, especially, the right results."