Both sides had chances early in the game, but it was the visitors who broke the deadlock in the 28th minute when Daniel Parejo was brought down inside the penalty area, allowing Roberto Soldado to fire the ball in from the spot.
The 27-year-old netted his second just six minutes later, tapping in an Andres Guardado cross from just in front of the goal.
Valencia extended their lead in the 62nd minute, as Guardado fired the ball in, having seen a previous effort saved just seconds earlier.
Both teams continued to push for a late goal, but solid defending at both ends restricted chances until Nelson Valdez popped up deep into stoppage time to round off a strong performance for the visitors.
The result moves Valencia into the top four in the table, while Vallecano sit 10th.