Diego Costa struck the opening goal of a difficult night on 59 minutes, and then Raul Garcia doubled the lead just moments after coming onto the pitch.
Costa missed a penalty and then scored his second attempt from the spot to round off a victory that will further bolster Atletico's title hopes.
Miroslav Djukic's side produced a resilient defensive display for the opening hour but once they went behind they had no answers, while Simeone's men craved more goals, and went and got them.
Los Rojiblancos controlled the game for large parts but did not have their opponents on the ropes in the first half, only creating half chances, the best of which fell to Arda Turan, who narrowly failed to get on the end of a cross from Costa after 10 minutes.
Djukic's side were set up to frustrate the hosts and did a good job of it too, positioning themselves on the edge of the area and blocking any attempts to get through. They offered little in attack, their only dangerous moment a cross from Jonas which Thibaut Courtois struggled to deal with before finally gathering.
Atleti had more urgency after the break.
Costa forced a save from Diego Alves just three minutes after the restart, Arda sent a shot over the bar, and David Villa was inches away from directing a backheel from Arda in.
The deadlock was broken just before the hour mark.
Costa drove forward from the left wing into the box and took his shot early and Alves, perhaps distracted by the incoming Villa, was unable to keep it out.
The crowd inside the Calderon had been getting louder and louder with every chance wasted and once the ball hit the net, the stadium erupted.
Villa was replaced by Raul Garcia just after the goal and the former Osasuna player did not take long to get into the game, thumping the ball into the far corner of the goal as he attacked down the right-hand side.
Atletico were not finished just yet. Dorlan Pabon got in the way between Arda and the third goal, and then the hosts were awarded a penalty when Victor Ruiz knocked Costa over as he approached goal.
The Brazilian-born forward sent the spot-kick straight at Alves, who saved easily.
It was the third time this season Costa had missed from the spot but the home fans responded by encouraging their hero, and a few minutes later he won a second penalty, this time tripped by Antonio Barragan, and slammed the ball into the top corner.
Atletico needed one more goal to go top of the league and pursued it like they would a match winner but in the end they had to settle for three.