The defender's header on the hour mark was enough to seal all three points for the champions as they look to keep pace with Luis Enrique's side at the top of La Liga
The Brazilian defender was on target in a disappointing 2-2 draw with Celta Vigo on Saturday and took his tally to three goals for the season with a second-half header to secure all three points in Andalusia against a side who have proved problematic in recent seasons.
Atletico had never won in five previous visits to Estadio de los Juegos Mediterraneos, including a 2-0 defeat last term, but did enough to secure victory, despite not being at their best.
The defending champions were lacking a spearhead in attack in the absence of Mario Mandzukic, who is recovering from a broken nose, but coach Diego Simeone got the clean sheet he asked for as he watched from the stands serving a touchline ban.
Goalkeeper Ruben pulled off some fine saves for the home side, who were brought back down to earth following their 2-1 win at Real Sociedad at the weekend, but was unable to prevent Simeone's men securing their third league win of the season.
Atletico captain Gabi dropped to the bench along with Cristian Ansaldi and Raul Jimenez as Guilherme Siqueira, Raul Garcia and Mario Suarez came into the starting line-up.
Mane replaced the suspended Sebastian Dubarbier in the Almeria side, while Fran Velez and Wellington Silva also started in place of Edgar Mendez and Thomas Partey, who was ineligible to face his parent club.
Atletico were not allowed to settle in a frantic first half, but Antoine Griezmann ought to have done better with a tame header after Mario Suarez picked him out just seven minutes in.
Almeria were then fortunate not to be punished for some slack defending when Ruben kept out a downward header from an unmarked Diego Godin with his feet.
Simeone's side started to get into their stride and Tiago let fly with a long-range strike that forced a fine reflex save from Ruben just before the half-hour mark.
Ruben then came to Almeria's rescue once again five minutes before the break, palming away a left-footed strike from Raul Garcia following a slick Atleti move.
Saul Niguez replaced Suarez at half-time and Simeone's side continued to look the more likely to open the scoring early in the second half.
Griezmann beat the offside trap, but the France forward was indecisive as Ruben raced off his line to narrow the angle and the chance passed.
Atleti had looked dangerous from set-pieces throughout and it came as no surprise when it was an inviting corner from Koke that provided the opening goal.
The Spain international swung the ball over with pace from the right and Miranda rose highest to head home at the near post on the hour-mark.
The impressive Ruben produced another excellent save to deny Arda Turan a second goal 68 minutes in after the Turkey winger had cut in from the left at pace.
Verza fired a late free kick narrowly wide as Almeria applied some late pressure, but the visitors stood firm.