The Ghanaian striker has broken his goal drought since joining the Spanish side.
Coke Andujar registered the opening goal for the hosts in the 80 minute.
Before, Raphael Dwamena who picked the ball from his own goal area raced in a swift counter break to seal victory with goalie having already committed himself in the 93 minute of the game.
The former FC Zurich striker has been struggling for playing time since he joined the Spanish side from Switzerland during the summer.
He has fallen down the pecking order at Levante, he is expected to regain his confidence and devastating goal scoring form back after recording his first goal for the side.
Dwamena's first goal for Levante means they will now progress to the Round of 16 of the competition after their win in the Round of 32.