Atletico's last double over Real in the league came back in the 1950-51 season, which they finished as champions, but Diego Simeone's men came close to repeating the trick on Sunday.
The hosts, three points behind leaders Real in the table, got off to a miserable start as Karim Benzema found the net from close range.
However, after Diego Costa was controversially denied a penalty when he appeared to be clipped by Sergio Ramos, Atletico turned things around courtesy of Koke's fierce finish in the 28th minute and a sensational long-range strike from skipper Gabi just before the break.
Atletico had two further penalty appeals turned down in the second half and saw coach German Burgos sent to the stands for confronting referee Carlos Delgado.
Real then snatched a dramatic late leveller, Ronaldo scoring in the 82nd minute to extend his side's unbeaten run to 28 games in all competitions.
In the build-up, Atletico head coach Simeone claimed Real came into the match as the "most feared" side in Europe and they lived up to that billing early on by grabbing an early lead in an ill-tempered affair at Vicente Calderon.
In just the third minute, Benzema broke the Atletico offside trap to prod Angel Di Maria's exquisite inswinging cross past the static Thibaut Courtois.
Referee Delgado incurred the wrath of Atleti after 12 minutes as he refused to award a penalty after Ramos looked to have tripped Costa, and objects appeared to be thrown towards the official as a result.
Atletico were able to restore parity in the 28th minute, however.
Arda deceived the Real defence as he turned his way into space on the edge of the area, before slipping a pass into the box for Koke, who drilled into the bottom-left corner.
Real soaked up considerable pressure at the end of the half, but Atletico ultimately took the lead as Gabi hit a ferocious 40-yard effort through a crowd of players and goalkeeper Diego Lopez was unable to react quickly enough.
Costa missed a huge chance to double the advantage seven minutes after the break as he latched on to Koke's pass over the Real defence, held off Pepe and then fired wide with only Lopez to beat.
Atletico had two more penalty claims turned down just after the hour as Costa was involved in tangles with Pepe and then Alvaro Arbeloa.
The forward was booked for simulation following the second incident, drawing an enraged reaction from Atletico coach Burgos, who was sent to the stands for his angry protests.
Ronaldo spared Real's blushes as he rifled in a low shot from the centre of the area after Dani Carvajal's cutback, but the visitors were unable to find a late win despite piling on the pressure.
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