Karim Benzema had fired Real into a third minute lead when he converted Angel di Maria’s cross.
However, despite being denied a clear penalty when Sergio Ramos tripped Diego Costa, Atletico were in front by half-time thanks to fine strikes by Koke and Gabi.
Another turned down penalty appeal for a foul on Costa led Atletico assistant boss Mono Burgos to be sent to the stand as he tried to confront the referee midway through the second-half.
And Atletico were left to feel hard done when Ronaldo spun on the edge of the box to drill home a late equaliser.
A point for both sides means Real remain three points clear of Atletico, but Barcelona can move to within a point of Los Blancos should they beat Almeria later on Sunday.
Carlo Ancelotti’s men came into the game full of confidence after thrashing Schalke 6-1 on their return to Champions League action in midweek and took just three minutes to open the scoring.
A short corner from the right was worked back to Angel di Maria and his in-swinging cross was slotted home at the back post by Benzema.
The home fans and players were left incensed seven minutes later when Costa was tripped inside the area by Ramos, but referee Carlos Delgado Ferreiro waved away claims for a penalty.
Some of the Atletico players took their protests too far, though, as Arda Turan appeared to push Ferreiro and was lucky to only receive a yellow card.
That decision added fire to an already intense atmosphere inside the Calderon and the home support inspired Atletico as they went on to dominate the majority of the first-half.
However, Atletico were thankful to Thibaut Courtois for preventing the visitors from doubling their lead twice in quick succession as he saved from Benzema and a near post backheel from Ronaldo.
Atletico were level on 27 minutes when fine work from Turan teed up Koke inside the area and he smashed a low right-footed drive into the far corner.
Diego Lopez then had to be quick off his line to prevent Costa from a narrow angle moments later.
But the hosts did go in front in spectacular fashion in stoppage time at the end of the half when Gabi collected a short free-kick and fired high into Lopez’s top right-hand corner from 35 yards.
Costa had a great chance to make it 3-1 seven minutes after the restart as he raced past Pepe to a long ball over the Real defence, but his weak shot squirmed wide of the target.
At the other end Benzema was inches away from his second of the afternoon when he volleyed Modric’s cross wide.
More controversy was to ensure, though, as Costa appeared to bundled over inside the area, this time by Alvaro Arbeloa, but again Ferreiro didn’t point to the spot and instead booked Costa for diving.
That led to Burgos having to be visibly restrained from confronting the referee by Atletico players and officials as he was sent to the stands for protesting.
The drama continued as seconds later Courtois had to be alert to parry Gareth Bale’s flicked header.
Ronaldo should have levelled 16 minutes from time when he headed wide when unmarked from Dani Carvajal’s cross.
However, the Portuguese made amends eight minutes later when he fired home a loose ball from the edge of the area to give Real a share of the spoils.