Levante pushed in search of an equaliser, and they very nearly found one when Andreas Ivanschitz was picked out inside the opposition box, only for his shot to be blocked.
Paco Jemez's charges doubled their advantage on 33 minutes, though, thanks to Baptistao's second of the night. Emiliano Insua picked out his teammate with a lofted cross, and the striker made no mistake to head the ball home.
Vallecano could have put the game beyond reach when they were awarded a penalty with 68 minutes played, but Alberto Bueno smashed the ball against the crossbar with his effort from the spot.
Levante failed to use the missed penalty to their advantage, with Vallecano comfortably preserving their lead to claim all three points.