Real played out an entertaining encounter and although two delicate finishes from Gareth Bale and Karim Benzema gave them a two-goal lead by the 25th minute, the hosts made it hard for themselves.
Mario brought Marcelino Garcia Toral's side back into the contest just before the break with a powerful finish, only for Jese Rodriguez to reinstate the two-goal deficit in the 64th minute.
An unstoppable Giovani dos Santos free-kick about 30 yards again put the pressure back on Carlo Ancelotti's side, but Benzema finished a deadly counter-attack in the 76th minute to wrap up the win, seeing them go top on goal difference.
Atletico generally controlled the first half against Almeria, but they found their hosts in a particularly defiant mood as they hassled and harried the visitors, who were without the injured David Villa, Thibaut Courtois and Luis Filipe.
Diego Simeone's men felt they were due a penalty as Javi Manquillo received a shove from Suso, but the referee waved away the claims as Atletico struggled to break through the hosts' rigid backline.
Almeria clinched the win in the final 10 minutes as Jose Verza first deceived Daniel Aranzubia with a cross before converting a penalty after the Atletico goalkeeper brought down Jonathan Zongo, earning a red card in the process.
Valencia moved up to eighth and heaped more misery on bottom club Real Betis in Saturday's early kick-off as they romped to a 5-0 hammering at the Mestalla.
The home fans were made to wait until the 41st minute for their first goal as Jeremy Mathieu scored, before Paco Alcacer netted for the third league game in a row, poking Eduardo Vargas' wayward shot in.
Just past the hour mark Sofiane Feghouli rounded off an incisive counter-attack with a confident finish just inside the area to make it 3-0, before Alcacer added his second and Vargas notched his first for the club to complete the rout.
Rayo Vallecano closed to within two points of safety as they cruised to a comfortable 4-1 win over visitors Malaga, with former Barcelona and Juventus youngster Iago Falque getting the first with a solo run before coolly beating Willy Caballero from a tight angle.
Anaitz Arbilla added another a few moments later in the 28th minute and after Sergio Sanchez picked up his second yellow card on the stroke of half-time, Joaquin Larrivey converted the resulting penalty.
With Larrivey turning provider, Falque scored a second eye-catching goal just after the hour and although Oleksandr Iakovenko pulled one back for Bernd Schuster's side, the hosts collected all three points.
