Montenegrin striker Bojan Kaljevic scored on his return after a long-term injury to hand Balzan a sixth consecutive win to make sure of starting the third round in third place, four points behind leaders Valletta.
Floriana, on the other hand, suffered the third defeat in six matches and will therefore start the next round in fifth place on 20 points.
The Greens lacked the injured Jurgen Pisani and the suspended Enrico Pepe and Antonio Monticelli while Ryan Fenech was missing for Balzan as he recovers from an injury. Bojan Kaljevic made his return on the field of play after an absence of almost ten months.
Balzan scored the all-important goal twelve minutes from time when off a cross by Alfred Effiong from the right, substitute Bojan Kaljevic headed home in style past goalkeeper Matthew Calleja Cremona.
BALZAN Ivan Janjusevic, Justin Grioli, Paul Fenech, Steve Bezzina, Samir Arab, Alfred Effiong (82′ Clive Brincat), Pedro dos Santos Calcado, Alexandar Vujacic (70′ Bojan Kaljevic), Dylan Grima (63′ Luke Sciberras), Alan da Silva Souza, Elkin Orlando Serrano Valero.
Subs not used: Christian Cassar, Lydon Micallef, Maxim Focsa, Sean Cipriott.
Coach: Oliver Spiteri
FLORIANA Matthew Calleja Cremona, Andre Scicluna, Steve Pisani, Clyde Borg (14′ Mario Fontanella), Mauricio Villa (67′ Conor Borg), Juninho Cabral (89′ Daniel Agius), Matteo Picciollo, Steve Bonnici, Manuel Briffa, Nicolas Chiesa, Marcelina Emerson.
Subs not used: Matthew Grech, Neil Spiteri, Jake Davies, Firas Aboulezz.
Coach: Luis Oliveira
Referee: Mario Apap
Assistant Referees: Mitchell Scerri, Roberto Vella
Fourth Official: Trustin Farrugia Cann
Yellow Cards: Bonnici, Juninho, Kaljevic, Pedrinho
Scorers: 78′ Bojan Kaljevic
BOV Player of the Match: Alfred Efiong