Alvaro Morata and Angel Correa scored a goal each in the first half as Atletico extended its biggest-ever winning run at home in the competition. Almeria pulled a goal back through Leo Baptistao in the second half.
Atletico moved to 34 points, even with fourth-place Barcelona ahead of the rival's home game against second-place Girona later Sunday. Atletico will have a game in hand after the weekend's round. Real Madrid, which drew 1-1 with Real Betis on Saturday, has a one-point lead over Girona.
Atletico was coming off a 1-0 loss at Barcelona in the previous league round. It had won 11 of its last 13 matches in all competitions before that defeat in Barcelona.
“We know there's still a long way to go. We lost the other day but it wasn't the end of it," Atletico forward Antoine Griezmann said. “We have to keep playing like this.”
Atletico's last setback at home in the league was a 1-1 draw with Getafe in February.
Morata opened the scoring on Sunday in the 17th minute after dribbling past a defender and then the goalkeeper inside the area. Correa added to the lead five minutes later from close range after a low cross by Marcos Llorente.
The assist for Morata's goal came from Griezmann, who had a goal disallowed for offside in the fifth minute. The France forward remains three goals shy of the 173 scored by Luis Aragonés, the club's all-time leading scorer.
Baptistão scored from close range for Almeria in the 62nd.
It was the 12th league loss for the club from southern Madrid, which remains the only team without a win this season. It stayed on four points from four draws. The Saudi-owned club this week was eliminated by fourth-division team Barbastro in the second round of the Copa del Rey.