Goalscoring chances during the opening 45 minutes were few and far between at the Campo de Futbol de Vallecas, with both defences on top.
As the second half progressed, visiting Valladolid became the dominant force and they eventually made that count with 19 minutes remaining.
However, their lead lasted just one minute as Jordi Amat sent the ball into the top right hand corner of the net from long range.
Despite having been pegged back, Valladolid continued to push forward and claimed what proved to be the winner in the 81st minute.
Beuno rounded Ruben in the Rayo goal before picking out Manucho, who rolled in his seventh goal of the season.
As the match drew to a close, Beuno had a chance to make the game safe for the visitors, but his strike from distance cannoned off the crossbar.
The result has moved the away side up to 11th in the La Liga standings, while Rayo stay seventh.