Seddini finished second with 86 points after two rounds, behind Filipino Angelo Vientos, who won the gold with 120 points.
The bronze medal went to New Zealander Noah Skipps (53 points), ahead of Emirati Salmane Al Ouadhi, who finished fourth with 52 points.
Khalil Seddini had previously won the Mohammed VI Jet Ski Cup, held last November in Agadir.