Kosta Barbarouses grabbed the only goal of a tightly-fought game as Glory bowed out of the FFA Cup against Melbourne Victory at Dorrien Gardens.
The former Wellington man struck shortly before half time and despite applying some concerted late pressure and creating several fine chances, Tony Popovic's men were unable to force the Round of 32 tie into extra time.
Unfortunately the first half also saw Daniel Stynes limp off with an ankle injury having been handed his starting debut for the club, but there were certainly positives to be gleaned from the defeat, notably an impressive cameo off the bench from Diego Castro and another dominant midfield display from Neil Kilkenny.
And Popovic felt that there was ultimately very little to choose between his side and the reigning Hyundai A-League champions.
"It was competitive and we were well and truly in the game," he said.
" A bit of quality from Barbarouses was the difference.
"We finished the game very strongly, but in the end it wasn't enough.
"In the first half there weren't many chances for them or us and for the goal they did score, the ricochet fell to the right player for them and the wrong one for us.
"Trying to get our combinations working will take some time.
"When I assess the game, I'll have a think about what really was the difference today, but overall there wasn't much in it.
"We've certainly made progress and there were patches of very good football and I could easily have been sitting here still saying that it will take time after we'd gone through [to the next round]".
The game's first chance arrived after nine minutes when former Glory man Storm Roux headed a Barbarouses cross narrowly wide.
The hosts responded in kind soon after, Dino Djulbic rising highest to meet a Kilkenny free kick, only to see his firm nod-down flash past Matthew Acton's left post.
And it was from another pinpoint Kilkenny set-piece that Glory went even closer, this time Alex Grant just unable to keep his towering header on target.
Victory continued to threaten in open play, however and broke the deadlock seven minutes before the break.
Jai Ingham led a rapid counter-attack down the left before finding Josh Hope who in turn played in Barbarouses and the New Zealand international then rifled a fierce shot across Liam Reddy into the far corner of the net.
After a cagey opening, the second half burst into life on the hour-mark when Kilkenny's thumping effort from just outside the box cannoned off the inside of the post and back out with Acton beaten.
The introduction of Castro from the bench then sparked further life into the home side who proceeded to enjoy their best period of the game.
Victory found themselves on the back foot as Glory surged forward, often prompted by the ubiquitous Kilkenny.
Substitute Jake Brimmer threatened the away goal with a free-kick that flew just over the bar before Djulbic drew a fine save from Acton having been picked out at the far post by Castro.
As the final whistle drew nearer, the men in purple forced a string of corners which had the Victory defence stretched to breaking point, but despite the backing of a vocal home crowd, they were just unable to find a way through.
FFA Cup Round of 32
Perth Glory 0 Melbourne Victory 1 (Barbarouses 38')
Referee: Shaun Evans
Perth Glory: 33.Liam REDDY, 2.Alex GRANT, 4.Shane LOWRY, 5.Ivan FRANJIC, 6.Dino DJULBIC, 15.Brandon WILSON (20.Jake BRIMMER 70'), 18.Daniel STYNES (11.Brendon SANTALAB 39'), 21.Jacob ITALIANO, 22.Fabio FERREIRA (17.Diego CASTRO 59'), 23.Scott NEVILLE, 88.Neil KILKENNY
Substitutes not used: 1.Tando VELAPHI, 3.Jason DAVIDSON
Yellow cards: Neville 3', Djulbic 16', Lowry 44'
Red cards: None
Melbourne Victory: 1.Matthew ACTON, 2.Storm ROUX, 3.Corey BROWN, 6.Leigh BROXHAM, 7.Kenny ATHIU, 8.Terry ANTONIS (10.James TROISI 80'), 9.Kosta BARBAROUSES, 14.Thomas DENG, 16.Joshua HOPE, 21.Carl VALERI, 23.Jai INGHAM
Substitutes not used: 20.Lawrence THOMAS, 26.Nicholas SETTE, 31.Benjamin CARRIGAN, 32.Thiel IRADUKUNDA
Yellow cards: Ingham 11', Deng 36'
Red cards: None