Messi, who appeared in court on Friday to answer questions relating to tax evasion, opened the scoring but lasted only 28 minutes before being withdrawn due to a thigh injury, with the club later confirming he will undergo scans on Sunday.
In his absence, Adriano added a second goal in an unusually low-key win for the Spanish champions.
Andres Iniesta's early effort was parried by goalkeeper Esteban and the Spain midfielder's cross was then headed wide by Gerard Pique.
But with just over 20 minutes on the clock, the breakthrough inevitably arrived as Messi cut in off his wing, exchanged rapid-fire passes with Pedro and smashed home a left-foot finish via the far post from in the 'D'.
Suso had Almeria's first chance but headed wide from Jose Antonio Verza's right-wing free-kick.
Messi then curled a shot over the bar from 12 yards in his last involvement before an early exit to be replaced by Xavi.
Alexis Sanchez sent an effort from the corner of the penalty area high and wide but Almeria showed signs before half-time of coming back into the game.
Rodri carried their main threat, volleying over from 12 yards and forcing a good save from Victor Valdes with another well-struck effort.
Defender Marc Bartra was first to threaten for Barca after half-time with a languid run into the Almeria half, but Alex Vidal tracked back with him to deny him a sight of goal.
Esteban judged his challenge well to deny Sanchez with his feet outside the box, but he was helpless to prevent Adriano stabbing home Cesc Fabregas' low cross in the 56th minute.
Pedro shot just wide from the edge of the box and Adriano was off target from similar range.
Almeria had the ball in the net in the 85th minute but the whistle had long gone for offside against Rodri, and he and Suso then got in each other's way as another chance went begging.
Barca substitute Cristian Tello shot wide when through one-on-one with Esteban, who then made a good near-post save from Dani Alves in injury time.
Barca's win was duly completed with the minimum of fuss, though there was a curious late confrontation between Valdes and Xavi which continued after the final whistle.