Gerardo Martino's side breezed to victory on Saturday to continue their 100% start to the Liga season
The triumph ensured that Gerardo Martino became the first Barcelona coach to win his first seven league games, but it came at a cost as their star man was forced off with a thigh strain eight minutes after opening the scoring in the first half.
Almeria offered no attacking threat in the second period at Estadio de los Juegos Mediterraneos and left-back Adriano capitalised to add the second after the break.
The hosts went into the match as the only side currently in La Liga to have never beaten Barcelona in the top flight.
Coach Francisco replaced Sebastian Dubarbier with Christian Fernandez as he plotted a way to end that run.
The Blaugrana eased to a 4-1 win over Real Sociedad last time out and Martino made three changes from that success.
Javier Mascherano, Xavi and Neymar missed out as Marc Bartra, Cesc Fabregas and Pedro came in.
The first 20 minutes were dominated by the champions, but they found breaking through Almeria's well-organised back line troublesome.
However, a moment of magic from Messi in the 21st minute gave Barcelona the lead.
The Argentine cut in from the right and fired a left-footed strike in off the far post, but his day would soon end in disappointment as the attacker was withdrawn, though he did manage to walk off the field.
Almeria created two good openings towards the end of the first half as Angel Trujillo nearly connected with Suso's inswinging free-kick and then former Barcelona B forward Rodri hit a stinging shot at Victor Valdes.
Barcelona appeared more focused at the beginning of the second half and Alexis Sanchez almost doubled their lead as he broke through on goal, but goalkeeper Esteban produced an excellent tackle.
The visitors were more clinical next time, however.
Fabregas got down the left side and played a low cross into the danger area for full-back Adriano to poke past the helpless Esteban in the 54th minute.
Another defender, Bartra, was involved in the very next attack and after a surging run through the middle, he laid the ball off to Pedro who hammered a shot just wide of the left post.
Adriano had a chance to get his second 13 minutes from time, but the Brazilian could only put his effort wide, while Barta should have got Barcelona's third when he missed the target from close range.