Jose Bordalas' side hadn't won any of their first five games back in LaLiga Santander but dealt a major blow to La Real's Champions League glances with victory on Monday night.
The hosts were given the opportunity to take the lead in the contest midway through the first half when Maxime Le Normand fouled Hugo Duro in the box.
Jaime Mata stepped up to take the penalty and stroked it to Alex Remiro's right, sending the goalkeeper the wrong way.
At first, the Belgian forward was flagged for offside but, after a VAR review showed that he was onside, the goal was given.
As both teams pushed for what would be a highly valuable three points, it was Getafe who snatched it as Mata stole in to score seven minutes from time.