Fernando Tissone tried to double the lead for Malaga, but his long-range effort was well stopped in the Valladolid goal.
With 20 minutes gone, the visitors started to dominate possession, and they were able to get back on level terms just after the half-hour mark after Daniel Larsson turned the ball in from a Manucho cross.
Tissone tried to restore the home side's lead early in the second half, but his shot from just outside the box went wide of the target.
Valladolid had a dominant spell as they looked to take the lead for the first time, but they were unable to create any clear-cut chances.
Malaga started to come back into the match in the final 15 minutes, as Santa Cruz pushed for his second of the game, but twice missed the target with headers.
The result leaves Valladolid in the relegation zone, while Malaga jump up to 14th.