Sogne Yacouba missed a penalty for the Porcupine Warriors but late goals from 16-year-old Matthew Anim Cudjoe and Richard Arthur were enough to secure maximum points at the Baba Yara Sports Stadium.
The fixture was played behind closed doors as Kotoko are serving punishment for hooliganism.
Arch-rivals Hearts of Oak scored two late goals to secure a 2-1 comeback win over city rivals Liberty Professionals in the Accra derby.
Michael Sefah stung the Phobians just 33 seconds into the game but an 86th-minute Bernard Arthur effort and Kofi Kordzi’s strike two minutes later secured all three points for Hearts, who have moved to ninth on the standings.
Liberty occupy the 10th position.
At the Accra Sports Stadium, Victorien Adebayor’s 86th minute goal spared Inter Allies’ blushed in what ended a 1-1 home draw with Wafa, who took the lead through Richard Acquah’s own goal.
Second-placed Aduana Stars returned to winning ways, following a 1-0 midweek defeat to Eleven Wonders, with a 2-0 home triumph over Legon Cities FC.
Yahaya Mohammed and Noah Martey were on target for the Fire Boys in Dormaa.
Medeama suffered their first defeat of the season with a 1-0 away loss to Dreams FC in Dawu.
Ibrahim Issah’s effort was the separating factor. Medeama have dropped to third on the standings.
There was a third consecutive home draw for Elmina Sharks as they were held to a 1-1 stalemate by Great Olympics.
Sulley Ibrahim’s goal denied the hosts all three points after Benjamin Bernard Boateng scored first at Nduom Sports Stadium.
The final match of the day, 12th-spotted Karela United and second-from-bottom King Faisal played out a 1-1 draw at Tarkwa’s Akoon Park.
Kwame Boateng broke the deadlock for hosts Karela but Mohammed Moustapha hit back for Faisal to level the score.
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Kofi Owusu’s 56th minute goal decided the fixture at the Obuasi Len Clay Stadium.
AshGold occupy the fourth position after their first defeat of the campaign.
Bechem United and Eleven Wonders with face off in the final match of the week on Monday.