Los Colchoneros have not won a Madrid derby since 1999, but with both sides set to meet again on May 17 in the Copa del Rey final, they seemed well on their way to reversing that streak after Radamel Falcao's fourth-minute opener.
But Juanfran's own-goal nine minutes later granted Jose Mourinho's men a route back into the game, and after a fierce contest with a number of bookings on either side, Angel Di Maria struck the game's winner just after the hour mark with an expert finish.
The win puts Madrid six points ahead of Atletico in second place, and gives them a vital boost ahead of their monumental Champions League task against Borussia Dortmund on Tuesday, with a 4-1 deficit to overcome.
Mourinho erred on the side of caution with his starting line-up, omitting Cristiano Ronaldo from the squad after a thigh complaint, while for Atletico, the game came too soon for Arda Turan and Tiago, with both midfielders finalising their recovery from injury.
With only four minutes on the clock, the home side were ahead. Diego Lopez could not smother a free-kick, and Diego Godin recovered the loose ball, clipping towards the far post for Falcao to head home.
And Atletico could have been 2-0 up before the 10th minute had Koke been a bit less selfish as he blasted into the side netting from a itght angle with team-mates queuing up in the box for the cross.
Madrid were struggling to gain a foothold in the game, but with 13 minutes gone, they drew level through no good work of their own. Di Maria’s free kick took an ungainly deflection off Juanfran, who could not stop the ball from bundling into the net.
Falcao nearly responded to put Atletico back in front minutes later, but after rising well to meet Koke’s devilish cross, he could not steer his header on target.
The match soon settled into the ferocious tempo befitting of a local derby, with tackles flying in left and right, forcing the referee into his pocket to fish out his yellow card no less than six times in the first half.
But minutes before the break, Madrid broke the Atletico ranks through Di Maria’s excellent run, allowing Karim Benzema to be slipped through, but his hesitancy gave Thibaut Courtois the split second he needed to nick the ball off the Frenchman’s toes.
The match restarted, and Diego Costa cracked a header off the crossbar, before Gabi inexplicably slotted wide with time to pick his spot as Atletico looked the more threatening side coming out of the break.
But just like the first half, Madrid found a goal despite appearing closer to conceding. Benzema spotted the darting run of Di Maria between the centre-backs, and played a neat pass to release the Argentine, who then slotted brilliantly into the far side.
Atletico responded as Costa’s run and cross was pushed away from danger by Lopez, before the Rojiblancos man was correctly denied a penalty for falling theatrically to the ground under pressure from Nacho.Late on, Filipe was released by Adrian Lopez towards goal, but could only find the side netting when other options would have been better served, as time simply ran out in the Madrid derby for Atleti for the 14th year in a row.