Joseph JoJo Ogunnupe opened the score on the 41st minute and Obinna Obiefule made it 2-0 on the 74th.
In another match, Fgura United and Zebbug Rangers shared the spoils in a goalless draw.
Naxxar lead the way with 32 points, followed by Qormi and Vittoriosa on 29, Senglea 26, Lija and Pietà 25, Mqabba and Sirens 23, Melita and Marsa 19, Zebbug 15, Fgura and Rabat 14 and Gharghur 9.