Levante had a 1-0 deficit from the away leg but took the lead on Wednesday night after 25 minutes with a goal from Nikolaos Karabelas.
However, Melilla pulled the aggregate scores back to 2-1, 1-1 on the night, just two minutes later when Chota found the net.
However, in the second half the favourites started to pull away. Roger Marti made it 2-1 in the 62nd minute, which became 3-1 15 minutes later thanks to Michel Herrero.
Vicente Iborra notched a penalty before Herrero was sent off for two yellow cards. However, Levante did enough for a 4-2 aggregate win.