Schuster revealed in the build-up to the match that he is to leave La Rosaleda after just one campaign in charge.
And the German managed to go out on a high, as Francisco Portillo's goal on the hour mark gave Malaga all three points in a game that meant little to both teams, who end the season in mid-table.
Substitute Jose Casado missed an injury-time penalty for Schuster's side, but that mattered not as Portillo's third Liga goal of the campaign proved enough in Andalusia.
Levante keeper Keilor Navas made a mess of a cross from the right, and Portillo was on hand to drive low into the net, despite the efforts of two defenders on the line.
The visitors' hopes of getting back into the game were dealt a big blow when midfielder Papakouli Diop was sent off for a second bookable offence 10 minutes from time.
And Malaga duly held on to round Schuster's reign off with a victory.
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