Atletico went into the game leading La Liga and looking to put the pressure on defending champions Barcelona - who play Sevilla on Sunday - but they met a resilient Almeria side and struggled against the relegation battlers.
Clear-cut chances were rare in the first half as Diego's speculative effort from just outside the area was as close as either side went, while Atletico were denied penalty claims just before the half-hour mark.
Jose Antonio Verza put Almeria ahead 10 minutes from time when his cross found the net and he doubled his tally six minutes later from the penalty spot, with goalkeeper Daniel Aranzubia sent off for hauling down Jonathan Zongo.
The result leaves Atletico on 57 points, level with Real Madrid, who go top on goal difference.
Atletico coach Diego Simeone was without key trio Thibaut Courtois, Luis Filipe and David Villa for the trip to Andalucia, all of whom missed out with injuries.
Fresh from their 3-0 derby disappointment against Real on Wednesday in the Copa del Rey, Atletico looked determined from the off and 19-year-old right-back Javi Manquillo almost got his first La Liga goal with a chipped effort in the seventh minute, but Angel Trujillo got back to clear.
January signing Diego was the next to go close with a dipping 25-yard effort, but Esteban got his fingertips to it, turning it past the post.
With 28 minutes on the clock, Almeria were lucky to escape without conceding a penalty.
The lively Manquillo once again found himself in an advanced position and on-loan Liverpool midfielder Suso pushed him in the back while challenging the teenager in the air, but the referee ignored the Atletico protests.
Diego narrowly missed the target again early in the second half as he cut across the Almeria area after coming in from the right before unleashing a powerful low drive towards the bottom-left corner, but the left-footed attempt went just wide.
Almeria substitute Helder Barbosa somehow escaped a red card with 24 minutes left as the Portuguese midfield produced a callous two-footed stamp on Tiago's right leg, resulting in his compatriot being forced off on a stretcher.
The hosts almost snatched the lead as Aleix Vidal jolted past two defenders before seeing his side-footed effort hit both posts, but luck was on their side shortly after as Verza fortuitously found the top corner after Aranzubia misjudged his cross.
Verza completed the scoring four minutes from time as he confidently dispatched a penalty past Atletico captain Gabi, who was forced to go in nets after Aranzubia was harshly sent off for bringing down Zongo.
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