The game was decided by an own goal in the 15th minute from Levante's Bruno Gonzalez, who deflected the ball into his own net as he tried to prevent it reaching Diego Costa after some fine work from Marcos Llorente.
Atleti should have added to their lead in the first half but after the break had to withstand plenty of pressure from Levante, who are playing their home games in the town of La Nucia while their Ciutat de Valencia stadium is being renovated.
Yet Diego Simeone's side saw out the victory to tighten their grip on third place by moving two points above fourth-placed Sevilla and six above Getafe in fifth, who drew 1-1 at Real Valladolid.
"We are very happy to win another game and the teams around us are dropping points so we're getting closer to our objective," said Llorente.
Llorente, who has undergone a radical transformation from a little-used holding midfielder to a highly effective second striker since the season resumed, was Atletico's focal point in attack before being substituted after an hour.
He engineered the breakthrough by latching on to a through ball and spinning away from two Levante players before cutting the ball towards Costa, with Gonzalez getting there first to knock the ball unwittingly into the net.
Costa could have doubled Atleti's advantage but headed wide while Yannick Carrasco and Thomas Partey kept Levante's keeper Aitor Fernandez busy.
Partey had a goal ruled out for offside early in the second half and the game changed when both coaches made triple substitutions, with Carrasco and Llorente making way.
Levante began to grow into the game although Atleti were still dangerous on the break and Joao Felix should have made sure of the points after an interception by Costa but the club's record signing blasted over the bar.
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