Msida managed to take an early lead thanks to Stacy Vella and although Marcelo Pereira equalised deep into stoppage time to force extra-time, Richard Attard converted a penalty to put the Saints in the third round.
In other matches, Zurrieq defeated Fgura United 4-0 in a game between two Second Division sides while Marsaskala beat Luqa St. Andrew’s 3-1 in a clash between two teams from Division 3.
St. Andrews beat Birzebbuga St. Peter’s 2-0 while Zejtun Corinthians defeated San Gwann 3-1.
First Division side Gudja United found no difficulty in beating Ta’ Xbiex from Division 3 while Second Division side Gzira United beat Sirens from Division 3 1-0 and St. Patrick defeated Marsa on penalties in two clashes between teams from Division 2 and teams from Division 3.
In another game between two teams from Division 2, Zebbug Rangers defeated Mellieha 3-0.