The last two meetings between City and Wellington had ended in scoreless draws and a third beckoned after no goals in the first half.
But former Socceroo striker Josh Kennedy's 61st minute close-range strike and a goal from Frenchman Harry Novillo off the Phoenix goalkeeper Glen Moss sealed the upset victory.
Phoenix's finishing woes continued as Melbourne City wrapped up only their second win in nine visits to Wellington.
The visitors broke deadlock after 61 minutes with Aaron Mooy's goal bound shot deflected in by Kennedy.
City pressed forward and were rewarded for their pressure in the 72nd minute when Slovenian Robert Koren's cross found Novillo, whose strike ricocheted off a diving Moss into the goal.
It was the Manchester City-owned Melbourne City's first final series victory in only their second appearance in the A-League playoffs.
City will face Melbourne Victory next Friday for a place in the grand final, while Adelaide United, 2-1 winners over defending champions Brisbane Roar on Friday, will face Sydney FC in Sydney on Saturday.