The hosts looked the better side for much of the soggy encounter, but the attacker took both his goals well to secure a crucial, if not convincing, victory.
Atletico Madrid was in pole position going into the weekend, but its defeat to Almeria on Saturday meant Barcelona only needed to win in Andalucia to retake the lead on goal difference, and it duly obliged in pouring rain, despite Sevilla's best efforts.
Alberto Moreno opened the scoring at the Ramon Sanchez Pizjuan when his 15th-minute shot was deflected in by Marc Bartra, but the hosts were unable to pull clear as they missed numerous chances.
Alexis Sanchez equalized with a clever header after 34 minutes, albeit from a seemingly offside position, and Messi put Barcelona ahead just before halftime with his first La Liga goal from open play since September 28 against Almeria.
Messi gave his side a two-goal cushion 11 minutes into the second half with another sumptuous finish and, although the hosts had their fair share of opportunities after, Barca claimed all three points, with Cesc Fabregas adding a late fourth.
Although Barca had more of the early possession, Unai Emery’s seventh-placed side deserved its initial lead, provided by Moreno.
Ivan Rakitic brought the ball into the area from the right flank before combining well with Diogo Figueiras. The ball then dropped to Vitolo, whose nudged pass allowed Moreno to hit a fierce shot that flew in off Bartra.
Sevilla came agonizingly close to doubling its advantage seven minutes later as Carlos Bacca headed against Victor Valdes' right-hand post from a devilish Rakitic free kick.
Rakitic also skewed wide after being fed into the area by Bacca and Sevilla was made to pay as the champions converted their first opportunity of the game.
Nico Pareja was harshly adjudged to have fouled Messi and, from the resulting free kick, Alexis knocked the ball past Beto with the back of his head despite appearing to be offside.
Barca scored again before the break. Diogo missed a tackle near the halfway line and Pedro capitalized by charging forward before cutting the ball back to Messi, who rifled into the bottom-right corner after teeing himself up.
Sevilla continued to spurn clear chances early in the second half, Vitolo stroking wide when one-on-one with Valdes in the 51st minute before Kevin Gameiro shot straight at the goalkeeper when pouncing on a rebound.
Messi then effectively wrapped up the win for Barcelona as he collected an Andres Iniesta pass on the edge of the area and coolly caressed the ball into the bottom-left corner, well out of Beto’s reach.
Bacca held off Gerard Pique before firing into the side netting as Sevilla sought a response, but Barcelona remained strong at the back and enhanced its flattering lead late on as substitute Fabregas cleverly dinked the ball over Beto after Alexis' cutback.