The FC Porto forward scored two penalties in the first half in addition to a goal in the second half. Sardar Azmoun scored Iran’s fourth goal.
Ma Hei-wai and Anthony Francis Pinto scored for the home team to help them keep pace with the Iranians.
The result leaves Hong Kong at the bottom of Group E with one point, having lost four games and drawn one.
Iran, meanwhile, tops the group with four wins and a draw.
The top two teams from the group move on to the third round of World Cup qualifiers in Asia while the bottom two head to the third round of Asian Cup qualifiers.