Cacau scored himself after the break and Gomez brought his season tally to 10 to secure Stuttgart's victory.
Abdelaziz Ahanfouf converted a late penalty for the final goal.
Wolfsburg began strongly against Frankfurt and Diego Klimowicz put the home team ahead after eight minutes.
But Frankfurt fought back with goals from Michael Thurk and Alexander Maier shortly after the hour, before Mike Hanke's header in the 73rd tied the game.
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