Goals from Rondon, Baptista and Maresca gave Malaga a huge boost in their bid to avoid the drop as Los Colchoneros capitulated at the Vicente Calderon.
Despite Atleti's valiant attempts to get something from the game late on, it was Malaga who scored again to add gloss to the win through Maresca's instinctive finish.
Both teams enjoyed prolonged spells of possession in the opening quarter of an hour but that mundane start to the game was broken abruptly by the Andalucians through a snappy counter-attacking move. Sebastian Fernandez and Julio Baptista linked up well, but the former saw his effort blocked thanks to some last-ditch defending.
Tempers then reached boiling point as Sergio Aguero went to ground in the box, but the referee waved away the passionate claims for a penalty. A number of players got involved in a heated argument as Pellegrini's stifling tactics were frustrating Atleti.
In the 28th minute, Los Boquerones took a surprise lead to silence the majority of the Vicente Calderon. Jesus Gamez supplied a tempting cross which Rondon gladly thumped into the bottom right corner leaving Davide De Gea with no hope of saving it.
The advantage was quickly doubled in the 35th minute through Baptista. The burly Brazilian clinically nodded in Fernandez's deep cross with only a narrow angle to aim for following a swift counter-attack catching out their naive hosts.
Quique Sanchez Flores' side went into the dressing rooms at half-time dumbfounded by their two goal deficit as the tactics employed by Pellegrini nullified the star-studded Atletico attack while exposing the hosts' defensive frailties.
Very little changed after the interval as Malaga snuffed out any opportunity which Atleti tried to make for themselves. Diego Forlan was introduced on the hour mark to breath some life into his team's efforts and immediately began to dominate possession and look more determined in their endeavours for a breakthrough.
A promising break for Los Colchoneros was stopped in its tracks as the referee harshly adjudged Dominguez to have fouled Malaga defender Martin Demichelis. Another counter-attack saw Forlan claim possession in midfield but after his excellent run, his shot was dragged disappointingly wide. A free-kick from the Uruguayan was then tipped over by Caballero in the visitor's goal as Atleti's attack wouldn't relent.
For all the home side's possession, Malaga broke yet again and the third goal finally arrived. A classic counter-attack saw De Gea get a strong hand to a powerful attempt but Maresca followed up in the 83rd minute to blast the ball home. Sanchez Flores' side still pressed on despite their latest setback but it proved in vain as the away side defended staunchly to retain their clean sheet.
The three points for Malaga see them rise to 13th in the Primera Division significantly easing their relegation fears. Atletico Madrid remain in sixth place, occupying the final Europa League spot as their Champions League qualification hopes have now fully vanished.