The federation's decision means Ronaldo, the top scorer in Spain top flight this season with 37 goals, can play in Saturday's game at home to Eibar. It was the Portugal captain's fifth booking and would have resulted in a one-match suspension.
Ronaldo was cautioned after the referee ruled he had dived to try to win a penalty although television replays clearly showed he had been felled by a Rayo defender.
"The RFEF Competition Committee has upheld the appeal submitted by Real Madrid against the yellow card shown to Cristiano Ronaldo in the match against Rayo Vallecano," the club said on their website.
With a win over La Liga debutantes Eibar, second-placed Real can close to within a point of leaders Barcelona, who play at fifth-placed Sevilla later on Saturday.
(Reporting by Iain Rogers, editing by Ed Osmond)
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