Barca took the lead after 20 minutes, when Messi played a neat exchange with Alexis Sanchez on the edge of the box before smashing a left-footed shot in off the post.
However, the little Argentine picked up a thigh injury just minutes later, forcing him to come off, with Xavi Hernandez introduced into the game in a somewhat surprising decision, considering Neymar’s presence on the bench.
Adriano slotted home a low Cesc Fabregas pass to make it 2-0 soon after, and Barca could easily have made it three through Cristian Tello in stoppage time.
The result puts Barcelona clear at the top of the Liga table for at least a couple of hours, as Real Madrid faced Atletico Madrid - the latter the only other side with a perfect record - later on Saturday night.
Tata Martino opted to play Pedro ahead of Neymar following the mid-week demolition of Real Sociedad, with Marc Bartra keeping his place in the centre of the Barca backline.
Almeria started the sharper of the two sides, unsettling the Barcelona defence with their pace and directness, but it was the visitors that took the lead after 20 minutes, when Messi played a neat exchange with Alexis Sanchez on the edge of the box before smashing a left-footed shot in off the post.
However, the little Argentine picked up a thigh injury just minutes later, forcing him to come off with Xavi on in his place.
Almeria grew in stature as the first half progressed, with Rodri coming closest to restoring parity, but the on-loan Barca forward struck his effort on the half-volley straight at Victor Valdes.
Barcelona took full control of the game after the break and pegged the hosts deep into their own half for long spells. Sanchez was unfortunate not to find the net after rounding Esteban, but the Almeria keeper did well to time his challenge perfectly on the edge of his own box.
Martino’s men quickly doubled their lead, with Adriano turning home a low Cesc Fabregas pass across the face of goal to make it 2-0.
With the game seemingly out of reach Almeria coach Francisco Rodriguez elected to withdraw key players Fernando Soriano and Aleix Vidal with important ties against fellow relegation rivals coming up.
Substitute Christian Tello almost made it 3-0 in stoppage time, racing through on goal after being slotted through from deep. But after opening up his body the winger planted his effort wide of the post.
Man of the match – Marc Bartra (Barcelona)
The young centre back has been overlooked by a series of Barcelona coaches, but he grabbed his chance with both hands today. Bartra looked assured at the back against a fast and tricky Almeria attack, also surging forward in the style of his defensive partner Gerard Pique to cause chaos in the opposition half.
Almeria – Esteban 7, Nelson 4, Trujillo 5, Pellerano 5, Christian 5, Tebar 5, Verza 6, Vidal 7, Soriano 7, Suso 7, Rodri 7. Subs – Dubarbier 4, Azeez 4.
Barcelona – Valdes 6, Dani Alves 5, Bartra 8, Pique 6, Adriano 6, Busquets 6, Iniesta 7, Fabregas 7, Sanchez 7, Pedro 6, Messi 6. Subs – Xavi 6.