Jose Antonio Verza curled in a stunning goal - surely meant as a cross - 10 minutes from time after Almeria's stubborn defensive display had driven Atletico to distraction on a night of pure frustration.
And things got worse five minutes later when goalkeeper Daniel Aranzubia - perhaps at fault for the opener - blundered in a big way, fluffing a back-pass and then fouling Jonathan Zongo to concede a penalty, converted by Verza, and seeing red.
Atletico ended the night in second place in the overall standings - if only on goal difference following a big win for Real Madrid - but victory for Barcelona at Sevilla on Sunday would send Gerardo Martino's men back to the top of the league.
Under that scenario, all three title challengers would be on 57 points after Real dispatched Villarreal.
Karim Benzema scored twice and Gareth Bale marked his return from injury with a goal and an assist in a 4-2 win where Cristiano Ronaldo's absence hardly mattered.
Having spent considerable energy on attempting to repeal the three-match ban handed to the FIFA Ballon d'Or winner, Madrid were turned down and had to field a side to face Villarreal without their talisman.
Not to worry, they had Benzema, Bale, and Jese, who all got their names on the scoresheet.
Paco Alcacer scored twice as Valencia followed up their Nou Camp heroics by thrashing lowly Real Betis 5-0 at the Mestalla.
Having beaten Barcelona in their last outing, Valencia began positively and took the lead after 41 minutes through a header by Jeremy Mathieu.
Alcacer doubled Valencia's advantage on the stroke of half-time, and added his second in the 67th minute, soon after Sofiane Feghouli had made it 3-0. Eduardo Vargas marked his full debut for Valencia by scoring the fifth goal with 11 minutes remaining.
Rayo Vallecano breathed life into their hopes of avoiding relegation with a resounding and morale-boosting 4-1 win over Malaga, who had to play the entire second half with 10 men.
Tottenham loanee Iago Falque broke the deadlock midway through the first half with a fine individual goal and a deflected effort by Anaitz Arbilla just a minute later doubled the hosts' advantage.
Joaquin Larrivey slotted in a penalty on 45 minutes and Sergio Sanchez was given a second yellow card for conceding the spot-kick.
Rayo then coasted to victory, Falque scoring another impressive goal but Ukrainian forward Oleksandr Iakovenko got a late consolation for Bernd Schuster's side.