The game looked set to end after 90 minutes but an Oskar Zawada goal in the ninth minute of added time kept the home side in the game.
It was a frustrating night for the Phoenix and their fans who had been hoping for a first grand final appearance.
Against the run of play, Victory took the lead in the 81st minute when Adama Traore scored with a long-range shot.
The Phoenix had dominated all aspects of the game but without a goal, until Zawada's strike which kept the fans in their seats for another 30 minutes.
The home side should have gone ahead in the 61st minute but captain Alex Rufer had his penalty, for hand ball, saved by Victory keeper Paul Izzo.
The excitement of the equaliser did not last long for the local fans, with Victory substitute Chris Ikonomidis scoring from a corner in the first-half of extra time.
While the Phoenix continued to press and get into good scoring positions, they could not find a second equaliser.
The game was there for the taking for the Phoenix, who dominated across the park but not on the score sheet.
Influential Phoenix midfield Ben Old threatened the Victory goal on numerous occasions and hit the woodwork during one of many raids into the opposition area.
Kosta Barbarouses went close in the first half but his shot went straight to the Victory keeper.
However, it was Traore and then Ikonomidis who broke the hearts of the sold-out crowd.
The Victory spent the majority of the game feeding off scraps, but made their two efforts count and they will now contend for a fifth A-League title against either Central Coast Mariners or Sydney FC.
A record season ends in disappointment for the Phoenix, they had their highest finish in the regular season, had their most points and wins, but did not get to challenge for that elusive first title.
The first leg in Melbourne last weekend finished 0-0.
The match was declared a sell-out on Friday, with the final attendance figure 33,297.
The other semi-final is between minor premiers Central Coast Mariners and Sydney FC with the Mariners leading 2-1 after the first leg.
