The Argentina superstar has now scored eight braces and one hat-trick in La Liga this season. He has not scored a solitary goal in any of his league games.
He has also scored braces in each of his last four games for Barca and eight of his last 11 games in all competitions.
Andres Iniesta and Cesc Fabregas wrapped up the points with goals quickly afterwards to end any hope of a Levante revival.
Martin Montoya came on in the 13th minute to replace Dani Alves after an injury meaning Barcelona fielded an entire team of La Masia graduates.
Barcelona dominated the first half but were unable to break down an extremely stubborn and disciplined Levante defence.
The hosts looked dangerous on the counter and actually had the best chance of the half when
Jose Javier Barkero was able to cut inside on the edge of the penalty area on to his left foot and send a powerful shot towards goal but Valdes was equal to it, tipping it over the bar.
In the second half Barcelona took control when Messi scored his 81st and 82nd goals of 2012 in the 47th and 52nd minutes.
His first came as Iniesta played a slide rule pass to the striker in the inside left channel and with his first touch the Argentine lifted the ball over the goalkeeper to finish.
Messi’s second came five minutes later with Iniesta again the provider as he ghosted past the defender and cut back to Messi who lashed the ball home.
Iniesta turned goalscorer just four minutes later after he cleverly used Jordi Alba’s run outside to cut in and thump a shot into the top corner from the edge of the area.
Fabregas then got Barca’s fourth as he and Iniesta played a glorious one-two inside the penalty area before Fabregas rounded the goalkeeper and finished from a tight angle.
Carles Puyol was contentiously adjudged to have handballed in the 88th minute but the penalty was saved by Valdes and he was quickly up to stop the follow-up too.
The Catalonians are now three points clear of their closest rivals Atletico Madrid at the top of La Liga.