Ivorian side, San Pedro halted Asante Kotoko's dreams of making it to the CAF Confederations Cup group phase.
The Porcupine Warriors lost by 2:0 in Abidjan in the return leg encounter after recording a 1:0 win in the first leg at the Baba Yara Sports.
Goals from Cheick Soumaro and Amede Diomande handed the home side victory in the play-off round second leg fixture at the Felix Houphouet Boigny Stadium in Abidjan.
San Pedro qualifies on 2:1 goal aggregates.
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.