Goals from Obed Owusu and Yakubu Mohammed were enough to end their five-game winless streak at home despite a late consolation from substitute Kwaku Asuandzie.
Kotoko coach Steve Polack maintained the lineup that eliminated Wassaman United in the FA Cup while the visitors' coach benched Paul Asare and Asuandzie.
The hosts had the first shot on target on the third minute through Seth Opare before Baba Mahama fired wide two minutes later.
Kotoko captain Amos Frimpong blocked an effort from Seth Amoateng on 18th minute and Kelvin Andoh headed wide the resulting corner-kick.
The hosts finally found a breach in the visitors defence by the 18th minute, when Obed Owusu jumped above his marker to head in Gyamfi's perfect corner kick to score his first goal of the season.
All Stars reacted to the goal but efforts from David Abagna, Andoh, and Jeffrey Degal were all dealt with by Kotoko goalkeeper Felix Annan.
After the break, Seth Opare played Emmanuel Gyamfi through but the latter's pull back was fluffed by Owusu.
Yakubu made it 2-0 by the 52nd minute, after he capitalised on a blunder by Sadiq Alhassan and fired past onrushing goalkeeper Rashid Seidu.
All Stars almost pulled one back on 48th minute through David Abagna but Awal Mohammed made a goal line clearance and hurt himself in the process. He was replaced with Awudu Nafui. Two minutes later, Asuandzie latched onto a through ball from Abagna and lobbed the ball past goalkeeper Annan.
All Stars coach Enos Adipah pushed his men forward in search of the equaliser but Kotoko kept their cool at the back and dealt with all the attacks.
Yakubu had an opportunity to score another goal for Kotoko after being played through by Baba Mahama in additional time but his effort was thwarted by Hafiz Adams.
Kotoko have moved to fourth position with 29 points while All Stars sit tenth with 24 points.