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.
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.
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.
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.
