Sluggish Atletico held at Elche in Cup opener
Thomas Partey had headed the visitors into an early lead at the Martinez Valero stadium as Atletico dominated before half-time.
However, after Luciano Vietto struck the post and Keidi Bare fired a great chance straight at Guillermo Vallejo, Diego Simeone's men were punished for their profligacy six minutes into the second-half.
Lucas Hernandez was controversially adjudged to have felled Lolo Pla inside the area despite appearing to play the ball, and Pla stepped up to send Miguel Angel Moya the wrong way from the penalty spot.
Vietto pulled another golden chance wide and Fernando Torres, on the night he equalled Luis Aragones's record of 368 appearances for the club, fired off target as Atletico failed to win away from home for the fifth time in the last seven matches.
Ponferradina scored the upset of the night as a stunning Sergio Cidoncha free-kick earned a 1-0 first leg lead over Villarreal.
Athletic Bilbao's poor form continued as they needed an equaliser from Raul Garcia to salvage a 1-1 draw at Balearic Islanders Formentera.
High-flying Leganes, who sit fifth in La Liga, carried that momentum into the Cup as Claudio Beauvue struck two minutes from time to win 2-1 at Valladolid.
And in the only all top flight clash of the night, Celta Vigo won 2-1 at Eibar thanks to John Guidetti's winner.