Sevilla go a point above Barcelona, who host Real Mallorca on Sunday, thanks to Youssef En Nesyri's early effort.
Barcelona stayed second but are level on points with both Sevilla in third and Atletico Madrid in fourth
On Tuesday, Atletico go to Old Trafford for a Champions League last 16 tie which is delicately poised at 1-1 after the first leg in Spain last month.
Oscar Trejo's penalty just before half-time was enough to seal victory for Rayo, who will now attempt to make their first ever final in the competition.
The stalemate reduced Madrid’s lead at the top of LaLiga from eight points to six at the end of the weekend, after second-placed Sevilla snatched a late victory over Atletico Madrid on Saturday.
The 21-year-old Vinicius has been a revelation this season and proved the difference again at the Santiago Bernabeu, where he went off to a standing ovation after securing Madrid their sixth consecutive victory.
LaLiga: Barcelona coach Ronald Koeman handed two-match ban after being sent off in draw against Cadiz
The Spanish Football Federation (RFEF) disciplinary opted to hand the Dutchman the shortest permitted suspension after his sending off in the final minute for arguing with officials as 10-man Barcelona limped to a goalless draw.
Frenkie de Jong was sent off in the 65th minute at the Ramon de Carranza stadium but holding on for a draw will earn little credit for Koeman, who was also shown a red card in injury-time.
Barcelona visit Cadiz in the Spanish league with pressure mounting significantly on manager Ronald Koeman.
Karim Benzema kept his scoring boots on from last season to bag a brace in win over Deportivo Alaves to get their LaLiga campaign underway.
A furious Diakhaby walked off the field after being involved in a heated exchange with Cala and claimed the Spanish player had used a racist slur towards him in the first half of Valencia's game in Cadiz three weeks ago.
Three goals in 10 minutes towards the end of the first half helped Madrid go top of the table on head-to-head, above Atletico Madrid, who play at home to Huesca on Thursday.
LaLiga: No evidence to support Mouctar Diakhaby’s allegation of getting racially abused by Juan Cala, says league
The league said it has analysed all the available video and audio of conversations between the two players, including hiring a company specialised in lip reading, but found no proof of racially abusive language.
Valencia reacted angrily to Cala's press conference, releasing a statement later on Tuesday entitled: "Juan Cala, we don't believe you."
LaLiga investigating Valencia's claim that Mouctar Diakhaby was racially abused, Javier Tebas confirms
"We are already carrying out an internal investigation with the videos and images of the game we have to clarify what happened," said Tebas.
LaLiga: Cadiz's Juan Cala, accused of racial abuse of Mouctar Diakhaby, wants to be presumed innocent
“Apparently the presumption of innocence doesn’t exist in this country,” Cadiz's Juan Cala told a Spanish television channel before stating that he will soon share his version of what happened.
Diakhaby had been involved in a heated exchange with Cadiz's Juan Cala before indicating to the referee David Medie Jimenez that he was leaving the field.
LaLiga: Atletico Madrid bounce back with 2-0 win over Villarreal; Real Valladolid draw 1-1 at Celta Vigo
An own goal from Alfonso Pedraza and Joao Felix's powerful strike gave Atletico a precious win after a wobble which had allowed Barcelona and Real Madrid to gain ground in the title race.
Barcelona had won their previous seven games and another victory would have put them back within touching distance of Atletico, even if LaLiga's leaders have played one game fewer.
LaLiga: Lionel Messi stars in Barcelona's 3-2 comeback win over Real Betis; Real Sociedad ease past Cadiz
Messi showed why Barcelona agreed to keep him an extremely rich man when on Sunday he acted as Ronald Koeman’s super-sub, scoring one goal and setting up another to help Barcelona earn a 3-2 win at Real Betis.