Jonathan Ruiz put the Saints ahead on 39 minutes but John Paul Muscat levelled matters ten minutes in the second half. Seven minutes later, Marlon Briffa put Mqabba 2-1 ahead and Claudio Calleja sealed the issue with a third goal two minutes from time.
In the second match, Dingli Swallows returned to winning ways as they beat Lija Athletic 1-0 thanks to a goal by Leontive Konda.