Wellington, who hadn't played at home in three weeks following an unsuccessful road trip across the Tasman that included defeats to Adelaide and Perth, made a shaky start to the contest.
They've been exposed out wide in defence all season and today was no different, although they scrambled well when they had to.
City had a handful of chances in the early stages, including one golden opportunity in the opening minute but Mate Dugandzic blasted his shot over the crossbar.
Despite their concerns at the back, it was the visitors who were even more careless when a loose back pass from City midfielder Erik Paartalu was pounced on by Nathan Burns in the 34th minute.
The former Australian international, who arrived in Wellington during the off-season in need of a second chance after a mixed spell abroad, grabbed his fifth goal of the season as the home crowd of 7410 came to life.
If Burns's strike awoke the fans from their Sunday afternoon haze, they reached full throttle quickly after when Roly Bonevacia produced a fine strike to score following a deft pass from Michael McGlinchey.
McGlinchey, who has been the Phoenix's best player this year, missed last week's loss to Perth due to the birth of his second child and his return was greatly received by his teammates.
The All White's delivery at set-piece is a feature of his play, while he is also dangerous in the open field.
After halftime, Burns added another as he took the lead in the A-League's golden boot race with a sharp finish from another McGlinchey assist.
By that stage the floodgates were open for a rampant Phoenix side who scored a fourth via a lovely Roy Krishna goal in the 50th minute.
Krishna hasn't always been a regular starter under coach Ernie Merrick but the Fijian international turned in one of his best performances in a Phoenix shirt during today's rout.
City later pulled one back from the penalty spot after Bonevacia brought down James Brown and striker David Williams did the rest.
But it mattered little in the grand scheme as Burns completed his hat-trick in final stages with a penalty of his own as he became the first Phoenix player to bag three goals in a game.
He is now two clear in the golden boot standings with seven goals for the season.
Wellington Phoenix 5 (Nathan Burns 34, 47, 85 Roly Bonevacia 40, Roy Krishna 50) Melbourne City 1 (David Williams 68) halftime: 2-0
