Sapong's first goal in the 18th minute off a defensive breakdown gave Kansas City a 1-0 lead, but Toronto got the equalizer in the 38th when midfielder Darel Russell got a ball past the left inside post.
Sapong added the game-winner in the 53rd minute on a header from Chance Myers, and SKC (14-9-6) won a third straight.
Toronto (4-15-11) stretched its winless streak to eight games.
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