Origi, the son of former Kenya international Mike Okoth, struck home in the 89th minute. The victors had taken an early lead through Simon Thorup in 17th minute before Tulio de Melo doubled the scores in 56th minute.
Origi featured in the entire match. Meanwhile, Dennis Oliech came in as a second half subsitute as AC Ajaccio were knocked out of the competition after going down 2-0 to Caen.
Both sides played to a barren draw in the first half before Mathias Autret broke the dead lock in the 63rd minute. Faycal Fajr then killed hopes for hosts Ajaccio with a second goal coming in 74th minute. The former Harambee Stars captain came on in the 57th minute to replace Claudia Dielna.