Medeama scored a late penalty to secure a 1-0 victory and condemn Kotoko to their first defeat of the season.
Kwame Boateng, who was sacked by Kotoko after a disappointing spell, converted the spot-kick to break Porcupine Warriors hearts despite all the efforts they made to pick a point.
Goalkeeper Felix Annan had pulled several top class saves to keep the scoreline blank but he could not keep out Boateng from 12 yards.
Boateng hit a powerful strike past Annan after referee pointed to the spot following a foul by Seth Opare on Rashid Nottey.
That was after a heavy downpour before the start of the second half had threatened to halt proceedings at the T & A park.
Medeama have moved to 4th with six points following the win while Kotoko now occupy the 7th spot with four points.