Kenneth Abela put the Corinthians ahead on 29 minutes and Adrian Carabott doubled the score on 92 minutes.
Incidents followed the second goal with a Naxxar official assaulting referee Paul Apap who was therefore forced to abandon the game.
The second semi-final between St. Venera Lightnings and Rabat Ajax will be played on Wednesday.
The final will be played on Sunday May 8th at the Hibernians Stadium.