Despite conceding an early goal and chasing the game for large periods, Los Blancos made it 10 successive wins over their fierce rivals and consolidated their position in the automatic Champions League spots.
The win puts Real six points ahead of Atletico in second place, and gives them a much-needed confidence boost ahead of Tuesday’s Champions League second-leg with Borussia Dortmund.
Jose Mourinho made nine changes to the side that were comprehensively beaten in Dortmund during the week - and it showed, as his makeshift defence crumbled after just three minutes. Gabi's free-kick was fumbled by Diego Lopez, who was once again selected ahead of Iker Casillas, and Diego Godin’s cross to the back post was headed home by the unmarked Radamel Falcao.
Against the run of play the visitors were soon level, however. Angel di Maria’s in-swinging free-kick flicked off the chest of the hapless Juanfran and nestled in the far corner despite the best efforts of Thibaut Courtois to stop an own goal.
Spurred on by their woeful recent record against Real and the opportunity to draw level on points with them, the home side had the better of the first period but struggled to break down a shaky-looking away defence.
Atletico’s dominance continued after the break and they should have taken the lead again when nice build-up play from Falcao created the opening for Gabi - but he inexplicably shot wide with just Lopez to beat.
Shortly after, the Colombian striker had a penalty appeal waved away after a clumsy-looking challenge by Michael Essien before Diego Costa cracked a header against the crossbar.
The hosts would go on to pay for their missed opportunities as Mourinho’s side landed the killer blow with half an hour remaining. Karim Benzema’s perfectly weighted ball gave the on-rushing Di Maria a chance to take a touch and compose himself before firing low past Courtois.
Late on, Filipe was released by Adrian Lopez and had several good options to pass, but he instead shot lamely into the side netting.
Atletico’s 14 years of derby pain will continue for a few weeks at least, but they’ll have the chance to right the wrongs when the two sides meet in the Copa del Rey final on May 17th.