The Phoenix had been just 18 minutes away from winning the minor semi-final at nib Stadium in regulation time, but Billy Mehmet's 72nd minute goal sent the game to extra periods.

Substitute winger Howarth then made the visitors pay for their failure to close out the game when he completed a brilliant one-two move with Scott Neville that got the Glory the winning goal and sent the 13,695 fans into raptures.

Victory sees Perth advance to the preliminary final where they'll face either Brisbane or Central Coast, with the Mariners their most likely opponent given they enter the second leg of the major semi-final with a 2-0 deficit.

A win in that fixture would be enough for the Glory to make the Grand Final for the first time since their 2004 National Soccer League title.

Earlier, Wellington had appeared on course for their second preliminary final appearance in just three seasons when Chris Greenacre and Manny Muscat both scored in the space of eight minutes early in the second half to cancel out Bas van den Brink's early opener.

Defeat ended Wellington's surprisingly impressive season and also brought an end to the career of Phoenix veteran Tim Brown, who had already announced he'd be retiring at the end of the campaign.

Wellington, who were also dreaming of making the decider for the first time, created little apart from their two goals and it wasn't enough to avoid a heartbreaking loss.

Perth went ahead just 13 minutes in when Tony Lochhead's clearance off the line travelled straight to van den Brink and the Dutch defender smashed it home.

After the Glory's appeals for a penalty when the ball deflected onto Andrew Durante's outstretched arm were rejected, the hosts nearly doubled their advantage when a delightful Liam Miller ball set up Mehmet but his volley went just wide.

The Phoenix lifted as the half went on and they got their reward just after the break when Brown used his chest to direct Bertos' cross to Greenacre and the striker finished with ease.

And the visitors hit the lead when Muscat cut in from the right flank and unleashed a wonder strike that curled inside the far post.

Just when it seemed Wellington were going to hold on for an upset win, they failed to clear a Dean Heffernan and Mehmet drove the subsequent flick on past Paston.

Perth had the run of play in extra time and made it count when Howarth linked with fellow substitute Neville and slotted it home to break Wellington's hearts in a win that was revenge for when the Phoenix eliminated the Glory in a 2010 penalty shootout.

Perth Glory 3 (van den Brink 13', Mehmet 72', Howarth 112')
Wellington Phoenix 2 (Greenacre 47', Muscat 55')
Crowd: 13,695 at nib Stadium