Trailing 0-2 after 60 minutes, the Phoenix delighted a record-breaking crowd of 14,421 by dominating the final half hour and deservedly snatching two late goals.
They stayed true to coach Ricky Herbert's positive intent and were rewarded when Daniel headed home from a corner in the 78th minute.
Six minutes later Melbourne were left stunned when Phoenix nailed another corner.
This time defender Tony Lochhead launched a far post cross that found Shane Smeltz unmarked at the edge of the 6m box for the striker to guide home a powerful header and tie the scores.
With their tails up the Phoenix then launched successive raids vainly searching to break the deadlock.
Phoenix skipper Ross Aloisi missed a chance with the last kick of the match after Smeltz fed him the ball on the right only for Aloisi to hastily shoot the ball wide and high.
It marked a pulsating final few minutes in a game dominated in the first spell by Melbourne as the Phoenix took time to settle.
Daniel Allsop, who scored five goals in Victory's grand final win over Adelaide United last season, proved a handful for the Phoenix defence in combination with left midfielder Carlos Hernandez.
Melbourne defender Daniel Piorkowski had a chance to score but his weak attempt from a corner was saved by goalkeeper Glen Moss.
Allsop had another chance when a mistake by Phoenix defender Cleberson gifted him the ball on the edge of the penalty box but the striker again lifted the ball over the bar.
The Phoenix played pretty soccer in midfield with their short passes but were unable to find strikers Vaughan Coveny or Smeltz, who were closely marked.
Victory had a more direct approach and were finally rewarded in the 18th minute when an Allsop shot hit Cleberson on the hand. Defender Kevin Muscat gave Moss no chance from the spot.
The Phoenix squandered a golden opportunity to equalise when they won a penalty after Allsop handled the ball in an attempt to clear a corner in the 38th minute.
Daniel's shot from the penalty spot hit the underside of the bar and his attempt at the rebound flew over the bar.
The Phoenix chased the game in the second half with a change in tactics.
They began moving the ball quicker, longer and wider and it resulted in Aloisi getting a chance but his stinger from 30m went wide.
Melbourne took advantage to score their second goal as Phoenix pushed up to find the equaliser.
Defender Joseph Keenan was the provider with a surge to the edge of the box where he slipped the ball to an unmarked Allsop, who rifled the ball into the goal
When Hibs, went up, to win the Scottish Cup - I wisnae there - furfuxake!
Botafogo - Rio de Janeiro and Wellington Phoenix, my two teams til death do us part.