Goals from Songne Yacouba and Safiu Abdul Fatawu were enough to win the Porcupines all three points in the Zone A top-of-the-table clash at the Baba Yara Sports Stadium.
The penultimate matchday win has seen Kotoko displace Medeama from the top of the table, with the latter dropping down to third spot.
The Porcupines opened the scoring in the 49th minute when Yacouba drove Fatawu's in-swinger into the lower bottom corner of the net.
The two men were once again architects of the second goal as Fatawu controlled a ball from Yacouba and released a shot into the net in stoppage time.
Elsewhere in Zone A, Ashanti Gold have taken over second position following a 4-0 thrashing of Bechem United in Obuasi. Amos Nkrumah, Appiah McCarthy, Shafiu Mumuni (penalty) and Douglas Opoku (own goal) handed all three points to the Miners. The Hunters are fifth on the table and have absolutely no chance of making the next round.
Fourth-placed Aduana Stars' hopes of qualifying have been dashed by a goalless draw away against second-from-bottom Eleven Wonders.
In Zone B, leaders Hearts of Oak, who have already secured a semi-final qualification, emphasised their supremacy with a 3-1 home victory over fourth-positioned and already-eliminated Elmina Sharks. Christopher Bonney (penalty), Abdul Manaf Umar and Mohammed Fatawu netted for the Phobians while George Amonoo registered his side's only goal.
Second-placed Karela United kept their hopes alive with a 2-0 triumph over third-from-bottom Dreams FC courtesy of goals from Solomon Sarfo Taylor and Patrick Yeboah.
In Cape Coast, third-placed Liberty Professionals picked up a 2-1 away win at Ebusua Dwarfs. Elvis Kyei Baffour's goal and then Simon Zibo's fifth goal of the championship proved vital. Razak Issah collected a consolation goal.
In Tema, Wafa's dreams were ended by hosts Inter Allies, who emerged 4-2 winners in their match-up. Samuel Armah's double and a goal each by Michel Otou and Fuseini Mohammed made the difference for the Eleven-Is-To-One. They conceded goals by Justice Aaron Amate and Ibrahim Abukari (penalty). Wafa have dropped to fifth on the table while Allies sit bottom despite the win.