The home side battled with only 10 men for 108 minutes of a goalless match that was eventually settled in favour of South Australian champions MetroStars with a 4-3 penalties victory at Frank Drago Reserve.
Bayswater City defender Jamie Coyne was dismissed after only 12 minutes following a tangle with MetroStars striker Perry Mitris. The officials did not see the initial incident but the defender retaliated and was given a straight red card by Adam Fielding after consulting his assistant.
"I thought our boys were magnificent today, going down to ten men so early, and we were the side that had the clear cut chances" Chris Coyne said.
"I'm immensely proud of my players. I thought they handled themselves well, and worked their socks off for each other."
After winning the Night Series, Cool Ridge Cup, league title and Grand Final this season, Bayswater's pursuit of a fifth trophy started to unravel from the moment Coyne's younger brother Jamie was sent off.
"The sending off was right," Chris Coyne said.
"Jamie has apologised to the players after the game, but the officials missed the first one. But he did lash out and the red card was there, but we had to deal with it and get on with it."
"I'm disappointed but overall you have to take everything into perspective, and maybe I'm being a greedy bugger and hoping for five. But fair play to them, they won it and they go on to next week."
"We showed another side of our game today."
"We are an attacking football team, but after the sending off we were disciplined and kept our shape well and hit them on counter attack and created some good chances."
"It's a credit to the players that they are prepared to dig in and work so hard for each other.?
With both sides locked at 0-0 after extra time, MetroStars keeper Daniel Godley was the hero saving two in the shoot-out to send them through to the next round and a trip to South Melbourne.
"It's a fantastic result for us, and I think everybody was on their last legs in the end" Godley said.
"But in a penalty shoot-out anything can happen. I'm just happy to make a couple of saves."
"Perth is never a good place to come to for me. I've been here with Adelaide City and the state team, and I've never won here in my life, so we're just stoked to come out on top today."
MetroStars coach Ivan Karlovic, who is leaving the club after this tournament, was delighted with the result on a hot and windy day.
"It was a difficult game in difficult circumstances, but both sides had chances and I thought it was good game all-round, and at the end of the day it?s a lottery in a penalty shoot-out," he said.
"Bayswater battled hard with 10 men and we did the same, so both sides can walk away with the heads held high. We have another trip to Melbourne next week and we?re looking forward to the challenge."
It was lively opening with both sides going close early. Mitris raced clear after only two minutes, but his lob from the edge of the penalty area drifted wide. Then on five minutes Todd Howarth played Gustavo Giron-Marulanda in on goal, but the Colombian striker's shot whistled over the top.
Bayswater had to reshape their side after Coyne's dismissal and MetroStars began to take control. Mitris found space down the left on 24 minutes, and his deep cross picked out Scott Tunbridge, who fired over from 6m.
Bayswater goalkeeper Devon Spence then came to his side's rescue on the half hour, saving well to deny former Adelaide United midfielder Fabian Barbiero. The Bayswater custodian was at it again before the break, this time denying Tunbridge's snap shot, and then pushing Joseph Polisena's shot around a post.
Bayswater opened the second half well. Howarth played in David Heagney, and with the MetroStars defence looking for an offside flag, that never came, Heagney?s lob from 10m drifted past the far post.
It was a great game with chances at both ends. MetroStars were denied by Spence again on 56 minutes, the keeper reacting well to tip Mitris' shot over the top, and from the resulting corner skipper Adam Van Dommele fired wide.
Moments later Heagney's long-range shot flashed wide. City were hitting on the counter attack, and when Adam Bachiller found space and played in Heagney, Godley stood tall to deny the striker.
The visitors pressed late in normal time, but again Spence denied them. First on 71 minutes, second half substitute Lawrence D'Arrigo raced clear from the impressive Barbiero's through ball, but his shot was well saved by Spence, and moments later Spence denied Antony Solagna's shot on the run.
In extra time both sides were out on their feet as the hot weather took its toll. But the visitors should have broken the deadlock on 104 minutes. Steven Grelli's free kick picked out the unmarked Mitris, who headed over the top from 3m with the goal at his mercy.
Godley then saved well from James Isaia's shot from the edge of the penalty area in the second period of extra time but they could not be separated and it was on to the penalty shoot-out.
Both sides scored their opening three spot kicks but Godley guessed correctly to save Sam Mitchinson's fourth, and the MetroStars custodian then saved Trent Kay?s fifth to win it.
PlayStation 4 National Premier Leagues 2014 Finals Series
Bayswater City 0
Northern Eastern MetroStars 0 (Won 4-3 on penalties)
Saturday 20th September 2014
Venue: Frank Drago Reserve, Bayswater
Attendance: 250 (Approx)
Referee: Adam Fielding
Assistants: Josh Mannella and Stuart Muldoon
Fourth Official: Matt Southern
Bayswater City: GK Devon SPENCE, 2 Declan HARGREAVES, 3 Adam BACHILLER, 6 Todd HOWARTH, 8 Paul MCCARTHY, 9 Gustavo GIRON-MARULANDA (10 Damien CATALANO 69?), 13 Trent KAY (C), 16 Jamie COYNE, 20 Sam MITCHINSON, 21 David HEAGNEY (18 James ISAIA 87?), 23 Chris SALDARIS
Subs not used: RGK Joel DRISCOLL, 14 Harry BISSETT, 19 Aaron DELANEY
Yellow Cards: Marulanda 64'
Red Cards: Coyne 12'
MetroStars: GK Daniel GODLEY, 2 David MENECHELLA, 5 Lee ROBERTSON, 6 Anthony SOLAGNA (16 Andrew ORPHANOU 110'), 7 Michael D'ALOISIO, 9 Steven GRELLI (15 Lawrence D'ARRIGO 63'), 11 Scott TUNBRIDGE (10 Andrew CIARLA 85'), 18 Fabian BARBIERO, 19 Joseph POLISENA, 21 Adam VAN DOMMELE (C), 23 Perry MITRIS
Subs not used: RGK Julian CALI, 3 Stefan CALI
Yellow Cards: Polisena 49'