Archie Thompson scored the winner in the 90th minute after capitalising on some brilliant work from his Victory teammates to earn the three points for the weary club.
Saturday night's match was Victory's third in nine days following a mid-week Asian Champions League clash against South Korean club Jeonuk Motors.
Thompson was one of four inclusions for the side which drew 2-2 on Wednesday night as Victory coach Kevin Muscat delivered on his promise to rotate his players in a bid to keep them fresh during a hectic schedule of A-League and ACL matches over the coming weeks.
Victory skipper Mark Milligan was credited with scoring both goals at either end of the pitch in the first half, including an own goal that handed Glory the lead after 27 minutes.
Michael Thwaite's low header from a corner ricocheted off the midfielder's knee and into the back of the net, sparking wild celebrations from the Glory defender.
Tom Rogic went close to equalising three minutes later after sidestepping two Glory defenders and fired on goal, but he could not beat the outstretched right hand of young goalkeeper Jack Duncan.
But Victory did square the ledger in the 40th minute after referee Shaun Evans awarded a penalty to the visitors when James Troisi was held in the box by Matt Davies as he charged towards goal.
Milligan made no mistake from the spot, calmly slotted the ball into the bottom-right corner.
Troisi had a late chance to snatch the lead for Victory, but his attempted volley went straight into the safe hands of Duncan.
The match appeared head for a draw after a dire second half until Thompson pounced on a clever pass from Troisi and hammered the ball past a hapless Duncan.
The last-gasp win was Victory's fourth from their past five A-League games and lifted the club above Western Sydney by one point on the table with four rounds to play.
Victory will now turn their attention to Tuesday night's ACL clash with Yokohama F. Marinos at AAMI Park.
Glory, meanwhile, remain winless from their past nine outings and appear destined to claim their first wooden spoon despite at one stage being 14 points ahead of Melbourne Heart.