New Edubaise United were unable to leave the Baba Yara Stadium unscathed as they conceded a late penalty.
The visitors were able to hold the Porcupine Warriors till the regulation time was exhausted but their luck ran out in injury time after Kotoko were awarded a penalty.
Defender Kwabena Adusei stepped up to convert the spot kick in the 92nd minute as Kotoko extended their perfect start to three matches.
The defending champions who have won all three matches this season are targeting a third straight Premier League success which would be unprecedented in their history.
Mas-Ud Dramani’s men sit at the apex of the table with nine points, two ahead of second placed team, Ashgold.
Herein are results of the Ghana Premier League played across eight centres at the weekend.
Kotoko 1-0 Edubiase
Inter Allies 2-3 Hearts
Becheem United 1-0 Dwarfs
Berekum FC 1-1 Medeama
Lions 2-1 Amidaus
Liberty 1-0 Faisal
Hasaacas 0-1 Aduana Stars
New Edubiase United on the other hand have gone three matches without a win and continue to occupy the bottom spot.
Their next game is a mid-week action against new entrants Inter Allies who are also winless in three matches.
Meanwhile, Kotoko will travel to Wa to face All Stars.