Mellieha missed the opportunity to secure promotion to Division 1 after suffering a shock 1-2 defeat to San Gwann on Monday.
Nikolai Filipov put the Blues ahead but Shaun Vella levelled matters for San Gwann. An own goal handed San Gwann victory.
Rabat are second on 37 points, followed by Naxxar on 36, Mellieha 35, St. Patrick 33 and Birzebbuga 31. Four teams will join Zejtun in Division 1 next season.
Meanwhile in another match, Mgarr United defeated Gzira United 2-0.