Getafe moved level on points with Malaga in fourth place thanks to Alberto Lopo's solitary second-half goal.
Neither side hit top gear in a pedestrian opening period but the game came to life after Lopo nipped in between Eliseu and Willy Caballero to head home Pedro Leon's corner 11 minutes after the break.
Malaga will feel they should have had an equaliser as Roque Santa Cruz lifted the ball over with a glorious opportunity moments after coming on, before Miguel Angel Moya produced a stunning save to turn Javier Saviola's fierce shot from close range onto the bar 12 minutes from time.
However, Getafe held on to register their third consecutive league victory despite having Diego Castro sent off in stoppage time for a soft second yellow card.
Getafe manager Luis Garcia had rebutted Manuel Pellegrini's claim before the game that the Madrid side were serious challengers to Malaga for the fourth Champions League spot, but there appeared to be very little between the sides as the hosts controlled the game for the first hour.
Alvaro Vasquez had an early penalty appeal waved away, whilst at the other end Moya had to be sharp to turn away long-range efforts from Ignacio Camacho and Isco, but there was far more in the way of goalmouth action after the interval.
Vasquez should have done better when he volleyed over within seconds of the restart and Joaquin also had an early opportunity to put Malaga ahead but he headed straight at Moya from Eliseu's cross.
The only goal arrived moments later as Lopo managed to get his head to the ball amongst a ruck of bodies at the near post to nod home his first goal of the season.
Angel Lafita came within inches of a second as the hosts looked likely to kill the game off on the counter-attack, but Pellegrini introduced Santa Cruz to play alongside Saviola up front with 25 minutes remaining and the visitors instantly looked more dangerous.
The Paraguayan really ought to have scored having been played in by Saviola seven minutes later but he tried to chip Moya from the edge of the area and the ball sailed over.
It was Saviola's turn to feel frustrated six minutes after that as he turned excellently onto Jeremy Toulalan's clever pass and smashed a shot that Moya somehow turned onto the bar.
Castro then wasted a great chance to make it 2-0 when he blasted over from six yards in stoppage time.
Seemingly still annoyed by that missed opportunity he stupidly brought down Jesus Gamez and was shown his second yellow card of the afternoon by referee Jose Luis Gonzalez.