The loss comes a day after the Bernabeu side - who remain in third place after the result - saw eternal rivals Barcelona celebrate their 26th La Liga title, and second straight, with a win over Alaves on Saturday.
The only goal came when Adri Embarba sent Real goalkeeper Thibaut Courtois the wrong way with a penalty midway through the first haalf, giving Rayo a deserved lead after an ambitious start in front of a typically raucous home crowd.
The hosts got the victor with a penalty kick converted by Adrian Embarba in the 23rd minute after a foul awarded by video review.
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The defeat keeps Zinedine Zidane's men on 65 points with three matches to play while Rayo moved up to 19th place with 31 points.
"Today we did nothing, from the first minute until the end, at all levels", said furious coach Zidane. "Sometimes you can not score, but today we did not even make chances, did not do anything in our play". I am angry, because the image we gave off today was bad.
"I have a very clear idea what I want to do, the players, profiles I want. We have to apologize to the fans and to the club".
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The end of the current season is expected to herald a drastic overhaul of the Madrid squad, who also suffered early eliminations in the Champions League and Copa del Rey prior to Zidane's arrival. "I'm upset because we didn't send the right message". We didn't play at all. Today it was everything, the attitude, everything. We did not offer anything in the duels or running. They put in the performance that we should have.
Asked if he would like the season to end now, Zidane said: "Yes, but we have to play these three games and do something different". I will always defend my players, but not today. "We can't be happy [with our display]". "They didn't create what I hoped they would". This happened today, but it is not just their fault.
Rayo: "They needed the points and they went out and got them".
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Positives: "We can't taking anything positive away from tonight, no. Nothing".