Mario Gaspar put the ball into his own net to put the hosts on the back foot early on, but Juanfran did the same with 12 minutes left on the clock to force a draw.
Mario Gaspar accidentally netted into the Yellow Submarine net in the opening minutes of the match, but Juanfran conceded a similar own-goal with just over 10 minutes on the clock to deny the Rojiblancos an El Madrigal win.
Diego Simeone's men stay second in La Liga following the first 1-1 draw with two own-goals in a decade, while Villarreal holds on to fourth place behind Barca, Atletico and Real Madrid.
The visitors unquestionably started the stronger as Juanfran whipped in a dangerous ball from the right with two minutes on the clock, which Gaspar met with his head but - unfortunately for him and his teammates - he headed past goalkeeper Sergio Asenjo into his own net.
Marcellino Garcia Toral's men went close to levelling the scoreline after 13 minutes, but Jonathan Pereira was unable to squeeze his effort on target after Cani fed him the ball inside the Rojiblancos' 18-yard box.
Atletico battled for supremacy and had a number of half-chances as the opening 45 minutes wore on, with Joao Miranda's header met by Asenjo's arms from a whipped free kick from skipper Gabi.
Diego Costa and David Villa were largely kept quiet as the hosts searched for a way to carve an equalizer, though the capital-based club dealt well with Villarreal's forays forward.
With halftime imminent, it was one-way traffic in the Yellow Submarine's favour and Mario nodded just wide as he blew a chance to make amends for his earlier own goal.
The second half began slowly as Villarreal passed Simeone's side off the park but the visitors kept all attacks in check - the hosts simply struggled the break through the defensive line.
Villarreal sent on Manu Trigueros and Javier Aquino for Tomas Pina and Hernan Perez in an attempt to forge a comeback with a third of the game to go, while Simeone withdrew Raul Garcia for Arda Turan.
With 23 minutes on the clock, Pereira threatened Thibaut Courtois' clean sheet once again but his effort to find the bottom corner was to no avail as his shot sneaked wide of the post.
However, the hosts finally had a stroke of luck on 79 minutes when Jeremy Perbet's run into the box resulted in a squared, low cross which Juanfran tapped past teammate Courtois into the back of the net as Uche celebrated as though he scored it.
Atletico seemed content to settle for a draw as Garcia Toral's troops pushed hard for a winner, but the hosts were unable to rustle the visitors' net for the second time in the match and it finished 1-1.