Messi was taken off in the 20th minute with a left hamstring problem and Barcelona subsequently confirmed he would undergo further tests on Monday, but the striker's exit had little effect on Gerardo Martino's side as they cruised to another comfortable victory.
Neymar opened the scoring in the 36th minute after combining with Cesc Fabregas, and Pedro finished a goal all of his own making a minute later.
Fabregas put the gloss on the scoreline with goals in the 63rd and 79th minutes, Jorge Molina's injury-time penalty no more than a consolation for Betis as Barcelona took advantage of Atletico Madrid's draw with Villarreal to extend the gap at the top of the table.
Both sides made a number of changes following midweek European games, the Betis team showing three changes and Barcelona bringing in six fresh faces.
The hosts started brightly, taking the game to their illustrious opponents, and Victor Valdes pulled off two superb saves in the 17th minute.
First, the Spain international denied Molina from point-blank range after the striker had got free on the byline, before rushing along his line to push away Juan Carlos' firm downward header from six yards.
A difficult start was made more problematic for Barcelona when Messi was withdrawn in the 20th minute after picking up an ankle injury in the build up to Carlos' chance.
Neymar then wasted a good opportunity for the visitors, sending a free header straight at Guillermo Sara from Dani Alves' right-wing cross.
The Brazilian atoned for that miss after Alex Song had threaded an accurate ball through for Fabregas. The Spaniard squared for Neymar, who had the simplest task of tapping home into an empty net.
Ninety seconds later the leaders went two up as Pedro picked the ball up inside his own half, knocked it behind the entire Betis defence and curled an exquisite finish inside the far post.
Barcelona almost went three up a minute before half-time but Neymar's pass was slightly behind Pedro and the Spaniard scuffed his effort into the ground and off target.
Betis started the second half as brightly as they had the first, Joan Verdu sending an effort just wide from the edge of the box before Nono thumped the post with a rasping drive from 25 yards.
Barcelona responded strongly and Betis were indebted to Sara for a double save to deny Neymar as the Brazilian looked to put the result beyond doubt on the hour mark.
The visitors did not have to wait long for a third goal, Fabregas tapping home from six yards following sumptuous approach play involving Andres Iniesta and Martin Montoya.
Fabregas claimed the fourth 15 minutes later, nodding Alves' cross in off the post, before Molina sent Valdes the wrong way from the spot following a foul in the area by Alves.
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