Siggiewi proved to be the better team during the first part of the match with Pierre Spiteri twice going close early on.
On 34 minutes Siggiewi took the lead with Pierre Spiteri heading in from a cross by Jason Camilleri.
Zejtun’s reaction produced a close-range shot by Dino Falzon with Vella bringing off a fine save.
Zejtun improved after the break as they went close on a couple of occasions. They also wasted a sitter through Brian Testaferrata.
Siggiewi increased their lead in the 76th minute through substitute Charlton Schembri.
Two minutes from time Zejtun scored a consolation goal through an excellent shot by Glen Azzopardi Busuttil.
Referee: Franco Cachia
Qrendi-St Venera L 0-0
St Venera Lightnings gained the point they needed to make it through to the quarter-finals on better goal difference than Qrendi.
The first half was a balanced affair with Qrendi going close after six minutes trough a low shot by Ronald Spina which was well saved by Caruana.
St Venera replied through efforts by Stephen Said and Justin Felice.
The Lightnings gained the initiative after the change of ends but they found it hard to penetrate the Qrendi defensive barrier.
St Venera were close through Mark Grech and Glen Micallef and late in the match a Johan Scicluna volley was saved with difficulty by Mascena.
Referee: Mohammed Khalil