Atletico forward Adrian opened the scoring in the 24th minute.
Turkey winger Arda Turan then the back of the net with a right-footed shot just before half-time.
Atletico are in second place with a record of nine wins, one loss and one draw, three points behind leaders Barcelona and eight clear of Real Madrid, who play later on Sunday.
With 13 points Azulones trail Levante by five for the final Europa League spot, and have compiled a record of four wins, six losses and one draws on the season.
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