The Argentina forward found the bottom corner to open the scoring from Martin Braithwaite’s backheel after the break.
The 33-year-old then doubled the lead 20 minutes later, finishing smartly after a wonderful solo run and pass from Dutchman Frenkie de Jong.
Jordi Alba wrapped up the win at the Camp Nou shortly after when he converted from Braithwaite’s header.
Messi’s double takes him top of the La Liga scoring chart with 18 goals, two more than Luis Suarez.
Barcelona are third in the table behind Atletico and Real Madrid, albeit having played a game more than the leaders.
Sevilla can also move back above them if they win their game in hand.