The game, originally scheduled for Sunday, was called off after 65 minutes while at a 1-1 scoreline following a heavy downpour which made movements impossible.
Kotoko made four changes to the side that started the abandoned game, with goalkeeper Ernest Sowah Sadick Adams, Eric Donkor and Awal Mohammed being replaced with Felix Annan, Yakubu Mohammed, Augustine Sefa and Evans Quao respectively.
Hearts, on the other hand, replaced Malik Akowuah, Bright Luqman, Cosmos Dauda and Richard Akrofi with Samudeen Ibrahim, Patrick Razak, Alex Kouassi and Fatau Mohammed taking their places.
Hearts unsettled their host in the opening five minutes but were unlucky not to open the scoring.
On the eighth minute, Hearts goalkeeper Ben Mensah made a double save to deny Kotoko from taking the lead after a quick counterattack. Obed Owusu latched on to a through pass from Baba Mahama and sent in a long range shot which was tipped to corner by Mensah, who then blocked the resulting kick.
Six minutes later, Razak fluffed an opportunity to put Hearts ahead when he connected a pass from Samudeen. The visitors then protested for Kotoko goalkeeper Annan to be sent off after tripping Razak on the edge of the box but the referee only showed him a yellow card.
Hearts brought on Paul Acquah to replace Kwame Kizito, who was involved in a collision with Owusu Jackson.
Baba Mahama had a chance by the 38th minute to put Kotoko ahead after Hearts goalkeeper Mensah punched Sefa's effort on to his feet but the former Techiman City star opted to square for Yakubu but the pass was cleared by Gnagne.
On the other end, Quao made the biggest save of the half to keep Kotoko from conceding, when substitute Acquah fired within the box.
Kotoko improved their performance after the break, making the visitors look uncomfortable at the back. However, Yakubu couldn't make their dominance count, missing several chances.
Ahmed Adams picked a knock by the 58th minute and was replaced by Richard Osei Agyemang.
Emmanuel Gyamfi almost found a breach in the Phobians' back-four. The former Ghana U-20 star dribbled past three Hearts defenders but his final pass to Yakubu was thwarted by Atinga.
The Porcupines brought on Sadick Adams for Yakubu on 67th minute, with Hearts’ Richard Akrofi replacing Leonard Tawiah.
Obed Owusu almost fetched the match winner against the run of play after linking up with Mahama's pass but the final effort could only hit the side net.
The game ended goalless leading the way for penalty shootouts.
Kotoko captain Amos Frimpong scored the first kick but Atinga saw his effort saved by goalkeeper Annan. Quao scored the subsequent kick for Kotoko only for Hearts centre-back Gnagne to send his into the skies.
Jackson scored for Kotoko to make it 3-0 and although Akrofi scored Hearts, Sadick won the day for Kotoko with a beautiful kick.
Kotoko and Hearts will now switch attention to the Ghana Premier League as the Porcupine Warriors host Medeama on Sunday while Hearts travel to Bechem to face Bechem United.