Enes Unal came off the bench to score two late goals for Villarreal, denying Atletico Madrid victory and dealing Diego Simeone's men a huge blow in LaLiga's title race.
Antoine Griezmann's controversial penalty had Atletico on track for a 12th win in 13 games in all competitions, the striker scoring from 12 yards at Estadio de la Ceramica after he was harshly adjudged to be brought down by Jaume Costa.
Jan Oblak had been mostly untested in the Atletico goal but when Alvaro Gonzalez stood up a fine right-wing cross to the back post, Unal was there to nod home a deserved leveller for Villarreal.
And in the first minute of added time, Turkey international Unal tucked home at the back post, Daniele Bonera's cross having made its way through a crowded box to find the unmarked striker.
Griezmann had earlier wasted a golden opportunity to secure all three points for Atletico, who are now 11 points behind LaLiga leaders Barcelona, who eased to a comfortable 2-0 win at home to Athletic Bilbao earlier on Sunday.
Atleti are winless in their last six league meetings with Villarreal and their title hopes, having been hurt by a narrow loss at Camp Nou earlier this month, now look over as Atleti imploded, Vitolo's stoppage-time red card compounding their misery.