Ronaldo's strike eight minutes from time ensured Real claimed a point against Atletico at Estadio Vicente Calderon to remain narrowly clear at the summit of the Primera Division.
Atletico, trailing Real by three points at kick-off, looked on course for the derby bragging rights after first-half strikes from Koke and Gabi had put them ahead following Karim Benzema's early opener for Real.
But Ronaldo lashed home in the 82nd minute to the relief of boss Carlo Ancelotti.
The result thwarted Atletico's hopes of completing a league double over their more celebrated rivals for the first time since 1951, having beaten them at the Bernabeu 1-0 earlier in the season.
Barcelona closed to within a point of Real after an emphatic, if not always totally convincing, victory over Almeria in the late kick-off at the Nou Camp.
Alexis Sanchez set the hosts on their way in the 10th minute before a superb Lionel Messi free-kick made it 2-0 inside 25 minutes.
A moment's sloppiness in the Barca backline allowed Angel Trujillo to pull one back for Almeria and at 2-1 Barca endured more than one or two nervy moments as the visitors probed for a leveller.
It took until the 83rd minute for Barcelona to finally put the contest to bed, Carles Puyol following up with a smart finish after Messi's header had come back off the bar, while there was still time for Xavi to inflate the scoreline further with a sumptuous fourth as Barca went above Atletico into second place.
Villarreal ceded ground to Athletic Bilbao in their bid to finish fourth as they were held to a 1-1 draw at home to bottom side Real Betis.
The hosts looked set to take all three points when Bruno Soriano gave them the lead from the penalty spot on 70 minutes, but the game changed 10 minutes later when Uche Ikechuwku was sent off for a second booking.
Betis then took advantage of having an extra man, Ruben Castro heading in the equaliser shortly after.
Substitute Kevin Gameiro's second-half strike was all that separated the teams as Sevilla claimed a 1-0 victory over Real Sociedad at the Ramon Sanchez Pizjuan.
Gameiro struck after 77 minutes to end Sociedad's two-match winning run as Unai Emery's Red and Whites moved up a place in the table to seventh.
Jagoba Arrasate's side, who were unfortunate to come away with nothing after enjoyed a dominant display after the break, remain in sixth.
A solitary goal by Joaquin Larrivey gave relegation-threatened Rayo Vallecano all three points against Valencia, moving the Madrid side to within three points of safety.
The Argentinian striker headed in on 61 minutes and Valencia were dealt a further blow when Antonio Barragan was sent off a quarter of an hour later for picking up a second booking.
Rayo remain 19th in the table but have closed the gap on 17th-placed Almeria to three points, while Valencia suffered their first defeat in six matches and drop to ninth.