Aidan Mizzi scored the all-important goal for the Amateurs six minutes from the end of the first half.
Qormi lead the way with 18 points, followed by Zebbug on 11, Sirens, Qrendi and San Gwann 10, Pietà and Zejtun 9, Vittoriosa 8, Mqabba 7, Zabbar and Melita 6, Marsa 3, Rabat 0 and Pembroke -1. Pembroke had ten points deducted.