Perth will meet Brisbane Roar in the A-League grand final after the Glory defeated Premiers' Plate winners Central Coast by penalty shootout in Saturday's preliminary final in Gosford.
The Glory will contest their first A-League decider next Sunday in Brisbane after a dramatic win in front of 7572 fans.
Scores were locked at 1-1 after regulation time and the defeat was a cruel one for the Mariners, with Patrick Zwaanswijk missing a second-half penalty and a host of other chances going begging.
They also appeared unlucky, the Mariners left fuming after Shane Smeltz's first-half equaliser to Adam Kwasnik's opener was allowed to stand despite clear suggestions of offside.
But the Glory had the final say, Jacob Burns netting the winner after Michael McGlinchey had fired a shot over the bar for the home side with the fourth spot kick.
It provided more heartache for Graham Arnold's Mariners, who went down to the Roar in penalties in last season's grand final.
The match failed to reach any great heights early, both sides making a cautious start and limited to just a handful of chances.
But Kwasnik brought the game to life in the 33rd minute when he put the Mariners ahead from Oliver Bozanic's corner.
There was a touch of fortune about the goal, with Travis Dodd getting the ball stuck at his feet and Kwasnik was on hand to smash in from close range.
The Mariners had little time to enjoy their lead, though, with the Glory hitting back inside two minutes in controversial circumstances.
Smeltz scored from close range after Billy Mehmet's cross, but replays showed Mehmet was just offside when played into space by Josh Risdon.
The Mariners almost regained the lead just after halftime with Tom Rogic forcing a good save out of Danny Vukovic and Josh Rose hitting the right upright from the rebound.
And they looked set to take the lead when Kwasnik earned a 53rd-minute penalty after a foul in the box from Steve Pantelidis.
Veteran Dutch defender Zwaanswijk stepped up to take the spot kick but drilled against the crossbar.
The Mariners continued to pepper the goal with Kwasnik coming agonisingly close on two occasions while they almost took the lead after a Vukovic blunder but McGlinchey's long-range free kick hit the bar.
The Glory almost stole victory against the run of play, with Smeltz wasting arguably the best chance of the game when having his unmarked header saved by Mat Ryan in the 84th minute.
Both sides tired in extra time, with the best chance falling to Rose, who had a curling shot tipped over the bar by Vukovic.