The Porcupine Warriors crashed out 2-1 on aggregate to see their Africa campaign end miserable.
Kotoko had to finish the game with ten men after defender Emmanuel Agyemang-Badu got sent off with two yellow cards.
San Pedro took the lead through a Soumaro free-kick in just the third minute of the game.
San Pedro eventually registered the second goal late in the game as substitute Diomande netted a 98th-minute effort.
Kotoko began this season's African campaign in the Caf Champions League where a first round loss to Etoile Sahel of Tunisia forced a demotion to the second-tier Confederation Cup championship.