Sydney FC and Adelaide United also began their new campaigns on Sunday and played out a 2-2 at Sydney Olympic Park Athletic Centre.
The Phoenix, last season's runners-up, looked poised to flip the script after Makala Woods opened the scoring at Hnry Stadium with her 51st-minute strike.
But Wellington's ill-discipline would prove their undoing, with Emma Main first clipping the feet of Taylor Ray in the penalty box.
Melina Ayres converted the spot kick in the 73rd minute, before 'Nix defender Lara Wall fouled Kelli McGroarty to give away another free kick in dangerous territory.
It was former Brisbane Roar midfielder Momo Hayashi's turn to step up and the Japanese dynamo delivered in the 87th minute with a wonderful strike.
"Football is cruel sometimes," Phoenix coach Bev Priestman said.
"It took them a penalty and a direct free kick to hurt us and we outshot them."
After claiming their fifth championship with a 3-1 triumph, City continued their winning ways over Wellington - having won all 10 league matches since 2022 between the two clubs.
City also extend their undefeated streak to 11 games, last suffering defeat in February, when they had a shock loss to Western Sydney.
Hayashi and Ayres are among the new faces in coach Michael Matricciani's squad after a raft of departures in the off-season.
Grand final hero and golden boot winner Holly McNamara (Everton) headlined the exodus, joined by midfielders Leticia McKenna (Nottingham Forrest), Leah Davidson (Charlton) and Laura Hughes (Southampton), defender Alexia Apostolakis (Bristol City) and Bryleeh Henry (Rosengard).
While Hayashi is embarking on a new era, Ayres is starting her second chapter at City, having signed her first professional contract with the ALW outfit aged 16.
The 27-year-old had left in 2017 and had various stints across the ALW, most recently playing at the Newcastle Jets.
World Cup hero Cortnee Vine also made her City debut after returning from the US.
Looking to go one step further this season, Wellington landed their own Matildas signing after luring Brisbane Roar icon Tameka Yallop across the Tasman.
In Sydney, the Sky Blues took the lead through teenage forward Asha Sutton, but scores were level in the eighth minute after a Charlotte McLean own goal.
The hosts retook the lead 10 minutes after halftime through Panama international Riley Cohn, who assisted their opening goal, but former Newcastle Jets and Western Sydney Wanderers midfielder India Breier netted with just two minutes left of regulation time.
Next up, the Reds host Perth Glory on Saturday and Sydney FC welcome Melbourne City on Sunday.
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