Mohammed Fatawu opened the scoring in the 40th minute for the leaders who later on saw a Nathaniel Asamoah toe-poke come off the crossbar.
Fatawu slotted in from close range, connecting Ahmed Toure's lay off. Kotoko enjoyed much of the possession and looked set to pick all three points.
But defender Awal Mohammed ended their hopes when he pulled an Amankwaa (CST) in the box as referee William Agbovi pointed to the spot.
Amankwah slotted to the opposite side of Soulama Abdulai, denying Kotoko all three points and earning the Gunners a share of the spoils.
This still put Berekum Arsenals under pressure at 14th position on the table.