The results meant the Ivorian side will proceed on a 2-1 aggregate to the group stage of the African second-tier club competition.
San Pedro took the lead as early as the 2nd minute after a sloppy start by the visitors.
The goalkeeping agility of Felix Annan was called into action midway through the first half as he denied the host from doubling their lead.
Coach Kjetil Zachariassen pushed more men into the midfield as Kotoko held on to end the half trailing by a goal.
With Kotoko needing to score to have any chance of qualification, Augustine Okrah was introduced into the game just after recess.
Despite several attempts, Kotoko failed to score that all-important away goal as San Pedro scored their second of the day to hit the last nail in the coffin for the visitors.
The Porcupine Warriors will have to wait another year to have any chance of ending the decades-long wait for a continental trophy.