Real said that the 29-year-old Brazilian had suffered a partial ligament tear in his left ankle and would miss up to six matches including his side's back-to-back Champions League Group F matches against Rosenborg Trondheim.
The club said that if his recovery went according to plan Ronaldo would be able to reappear in the Primera Liga match against Barcelona on November 20.
The Brazilian, who scored twice in the city derby, was carried off on a stretcher in the dying minutes at the Calderon after sustaining the injury when he put pressure on Atletico defender Luis Perea to turn the ball into his own net.
Right back Michel Salgado is out for 10 days after straining a thigh muscle against Atletico. As well as the matches against Rosenborg the Spanish international is also expected to miss the league games against Valencia and Deportivo Coruna.