Messi was replaced soon after opening the scoring in the 21st minute with his 11th goal of the season in all competitions, with Barca subsequently confirming he had suffered an injury to his right thigh.
The four-time world footballer of the year will undergo further tests on Sunday to determine the extent of the problem and how long he might be out for.
Barca are back in action on Wednesday when they take on Celtic in the Champions League.
Adriano, who scored Barca's second goal against Almeria as the Catalan giants claimed a club-record seventh successive Primera Division win to start the season, said in AS: "Hopefully it's nothing and he's with us for the coming games because he's a very important player.
"With him, it's a different team."
Barca coach Gerardo Marino added of Messi's injury: "Apparently Messi picked up small muscle strain in the back of his right leg when he scored. It's hard to say anything else until he undergoes additional tests."