The Cameroon international scored his 13th goal of the season when he turned past two defenders and fired high into the net after receiving the ball on the edge of the area from World Player of the Year Ronaldinho just three minutes from time.
The result left Barca 12 points clear of fellow Catalans Espanyol at the top of the table with two games left until the halfway mark of the season.
Espanyol visit champions Valencia on Wednesday, while third-placed Real Madrid, who have an extra game in hand, host Sevilla at the Bernabeu.
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Barca, who dropped their first points at the Nou Camp when they were held to a 1-1 draw by Valencia on Saturday, made a bright start against their modest opponents.
Ronaldinho manufactured the first chance after forcing a fine one-handed save from Levante keeper Juan Luis Mora with a powerful curling shot from the left, but Deco was closed down before he could follow up.
Levante, who had not won in their last six outings, gave as good as they got, however, and responded with a quick-breaking attack that almost ended up in a goal after Nacho beat the offside trap.
GOAL-BOUND SHOT
The midfielder rounded reserve keeper Ruben, who was deputising for the suspended Victor Valdes, but had his goal-bound shot cleared off the line by the retreating Damia.
Ronaldinho breached the Levante defence two minutes later and cut a neat pass back to Eto'o, but the striker blasted over the bar from the edge of the area.
The two forwards continued to put the visitors under heavy pressure and Levante conceded a dangerous free kick when Eto'o was brought down a few metres outside the area.
The quick-thinking Deco took the free kick while Levante were still organising a wall and his powerful shot flew past a helpless Mora after deflecting off Levante defender Alexis.
Levante refused to fold, however, and midfielders Nacho and Felix Ettien remained a constant threat on the break.
It was Ettien who set up the equaliser on the hour when he sliced open the Barca defence with a superb curling pass to Jofre and the Levante midfielder finished off with an angled shot inside the far post.
Levante had the ball in the net again 15 minutes later when former Real Madrid player Alberto Rivera clipped over Ruben but the goal was disallowed for offside.
But Barca upped the pace in the closing minutes and Eto'o deprived the visitors of a point when he snatched the win with his magnificent late strike.