The Citizens ended their commitments on seven points four ahead of Sliema Wanderers and Hibernians.
Abdelkarim Nafti put Valletta ahead but Andrew Cohen levelled matters for Hibernians during the second half. However Nafti notched the winner late in the game to hand Valletta victory.
Photo: Copyright © Stiefnu De Battista – sportmalti.com
MFA senior vice-president Ludovigo Micallef presented the cup to captain Ryan Fenech after the game.
The tournament comes to an end on Thursday with the clash between Sliema Wanderers and Birkirkara.