A horror five-minute period sees Wellington forgo early dominance as City finish clinically at Westpac Stadium on Saturday night.
It's a cruel facet of football that games turn on tiny margins, and Wellington Phoenix have paid the full penalty as Melbourne City bounce back to form in emphatic fashion.
With expected thunderstorms holding, Phoenix started brightly with Roy Krishna nearly finishing a fine flowing movement inside two minutes. Picking up the ball centrally he drew several defenders before feeding Kosta Barbarouses wide, whose well-whipped cross was tucked just wide by the flying Fijian at full stretch.
As the crowd observed a minute's appreciation for the recently departed All White legend Steve Sumner in the tenth minute, on the field Wellington almost offered the best possible tribute.
Barbarouses was again posing problems with his pace down Phoenix's right and his cross was deflected free to Krishna, whose shot cannoned off the knees of Thomas Sorensen to safety.
Returning to his old stomping ground, Manny Muscat almost became the villain for City as he appeared to catch Barbarouses with a trailing leg, and referee Jonathan Barreiro had no qualms in pointing to the spot.
Wellington's No.9 strode up confidently but struck his penalty against the apex of Sorensen's posts, to the joy of a small travelling contingent behind the goal.
Minutes later in the 18th minute Phoenix went agonisingly close once again - Krishna was felled just outside the box but referee Barreiro allowed play to run - Roly Bonevacia did brilliantly to skip past the last defender but his dinked effort rolled agonisingly past the far post.
Inside 60 seconds though it was City who cashed in. Nick Fitzgerald crossed in from the right and a horror double deflection off two Phoenix players left goalkeeper Glen Moss with absolutely no chance, as the ball squirmed home at the near post for an owl goal.
Muscat then clashed heavily with fullback Tom Doyle with replays suggesting perhaps a raised arm that could attract the post-game attention of officials. After some minutes receiving treatment the Nix left back however was cleared to return to play.
It went from bad to worse in the 29th minute when Moss was deemed to have handled outside the box - Luke Brattan played a low ball across goal which deflected fortuitously from Muscat's mistruck effort straight to Bruno Fornaroli, and the experienced marksman made no mistake thumping past Moss.
A heavy challenge on Krishna saw Muscat enter the book as his action-filled half continued, before Sorensen again saved well at the feet of Krishna.
Shortly after the restart it was Osama Malik in the book for a blood and thunder challenge on Krishna that left the star-striker prone for several minutes.
The Nix topscorer tried to play on, but went down shortly afterwards and was replaced by Shane Smeltz in the 54th minute.
Fine work from Josh Rose down City's left saw a ball whipped behind the Phoenix back four, with the slightest deflection cushioning it for Anthony Caceres to lash home City's third.
Academy graduate Sarpreet Singh came on for his first A-League appearance, and minutes later Barbarouses made amends for his penalty miss with a weaving, jinking run - nutmegging Brattan before finishing with aplomb past Sorensen.
It brought the crowd to life as Wellington attacked with greater intensity, and Doyle flashed a header just over the crossbar.
In the 79th minute space opened up for Doyle once more, and the fullback set off on a run reminiscent of his goal against Adelaide, but Sorensen proved equal to his driven shot.
With ten minutes to run some uncertain defending undid the revival, as two clearances in quick succession struck a City player, richochetting kindly for Kilkenny to lash past Moss.
Nicholas Colazo added the icing on the cake for City as with Doyle off the field injured a makeshift back four was undone, as City rubbed salt in Phoenix's wounds.