Real Madrid played some sublime football in the first half.
Navas then had to keep out a strike from Koke as the visitors looked to complete the turnaround at the Bernabeu.
Simeone's what-we-have-we-hold move nearly backfired when Bale skewed wide, while Sergio Ramos made his regular pitch to be Madrid's last-ditch hero - forcing Oblak to push a wonderful free-kick behind in stoppage time and powering over from the resulting corner.
Surprisingly, Ronaldo was withdrawn soon after that goal, much to the bemusement of the Bernabeu faithful, and with the Portuguese off the pitch, free-kick duties were left to Ramos who nearly snatched all three points in injury time when his set-piece destined for the top corner was clawed out by Oblak.
The Welshman was an unused substitute during Real's 3-0 Champions League win over Juventus on Tuesday, but comes in against Diego Simeone's men. It took Ronaldo to 22 goals in 30 career games vs Atletico and was also the 500th by anyone in a derbi.More news: Johnson plans to play it safe on eve of Masters
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The ex-Manchester United forward broke the deadlock with a stunning volley, before the 27-year-old fired home from close range four minutes later.
Thomas Partey's ball behind the home defence found Griezmann. Griezmann thus marked his 200th game for the club with his 108th goal, 18 of which have come in 20 games during 2018. Griezmann might have had scored earlier in the game if Costa, who had a frustrating afternoon, had spotted him eight yards out.
Atletico remain second on 68 points, four ahead of Madrid who occupy the third spot with seven games left to play in the league.
"Griezmann is a great player, he is very strong in these moments mentally", he added.