Emilio Cornago scored the all-important goal three minutes in the second half.
Naxxar lead the way with 27 points, followed by Qormi and Mqabba on 21, Lija 20, Senglea 19, Sirens and Vittoriosa 16, Melita and Pietà 15, Rabat 13, Marsa 12, Zebbug 10, Gharghur 9 and Fgura 8.