Jose Lucas Caetano Silva put Zebbug ahead on the 23rd and Hubert Vella doubled the score on the 44th with Ige Adesina reducing the gap on the 66th.
In another match, Pembroke Athleta and Zejtun Corinthians shared the spoils in a goalless draw.
Santa Lucia lead the way with 17 points, followed by Sirens, Vittoriosa, Zebbug and Mqabba on 12, Lija, Pembroke and Gudja on 10, Qrendi 8, Swieqi, Zejtun and Naxxar 7, Marsa 4 and San Gwann 0.