It took just nine minutes for the home side to open the scoring - Juanpi finding the bottom corner from close range after some sloppy defending from the away team.
Getafe continued to struggle in the latter stages of the first period and conceded a third two minutes before the half-time break when Charles finished off a move down the right.
Juan Rodriguez and Pedro Leon looked the most likely to make something happen for the visitors in the second half, but the damage had already been done as Malaga comfortably collected all the points on home soil.
The result has kept Malaga in 10th position in the La Liga table, but they are now 10 points outside of the bottom three. Getafe, meanwhile, remain just one place below their opponents.