Early in the 12th minute, Casemiro thought he had put Real in front when he headed home on a Toni Kroos free kick, however, following a brief review the referee overruled the goal due to offside.
Chances were few and far at either end and the points looked likely to be shared, but Nacho arrived in the box to head home with 12 minutes to go and put his side in the driving seat at a crucial stage in the title race.
Valladolid almost scored the equalizer when Sergi Guardiola fired high into the Madrid net from close range three minutes from time, but his effort was ruled out for offside as the points went to Madrid.
The loss sees Valladolid slip to 16th, while Zidane’s side leapfrog Barcelona and take sole possession of first.