Faisal, who were in the relegation zone before kick off, rallied from a goal down in the first half to beat the league champions in the outstanding match at the Baba Yara Stadium.
The defeat will Kotoko hopes of closing in on the top spot, though they have a game in hand.
Kwabena Adusei gave the Porcupine Warriors the lead after 42 minutes when he scored from the spot after Kotoko were awarded a penalty.
Kotoko held onto the lead to end the first half 1-0.
Thirteen minutes after recess, Faisal drew level when former Hearts of Oak player, Tetteh Nortey scored.
Kofi Owusu stunned the large Kotoko following at the stadium when he struck the match winner in the 88th minute.
Faisal are now out of the bottom three while Kotoko are placed fifth on the table.
