Matildas striker and league golden boot winner McNamara, 23, opened the scoring with a world-class long-range strike from the corner of the box in the 41st minute and added a second in the 43rd at AAMI Park on Saturday.
Fellow Matilda Leticia McKenna scored a terrific long-range goal of her own in the 49th minute, before Phoenix striker Makala Woods scored in the 52nd to give the strong Wellington fan contingent something to cheer about.
With her heroics, McNamara delivered City a premiership-championship double in front of 7174 fans and their first grand final win since the 2019-20 season, while denying Bev Priestman's Phoenix their first title.
Michael Matricianni's City draw level with Sydney FC on five championships and 10 ALW trophies overall.
City can yet claim a treble if they triumph in the Women's Asian Champions League.
They depart for Suwon on Sunday for Wednesday's semi-final against Japanese club Tokyo Verdy Beleza.
"I'm so proud of this group. To win the premiership was special but now to complete the double together is something we'll never forget," skipper Rebekah Stott said.
"This team has shown resilience, belief and togetherness all this season.
"But we know the job's not done yet. Tomorrow, we head to South Korea with a chance to chase something historic - a treble."
From the opening whistle City were on top with Shelby McMahon and McKenna running the show and McNamara a constant threat.
McNamara - who had gone goalless in her five previous ALW games including the two semi-finals against Melbourne Victory - Â had a goal disallowed for offside in the 38th minute, but struck three minutes later.
Danielle Turner curled a super ball towards McNamara and the striker worked the ball to Keane, then received it back and beat Esson with a sensational curling strike.
Two minutes later, McMahon brilliantly released McNamara down the right and the City striker burst forward to fire home her second.
McKenna snagged City's third when she was given too much space on the edge of the box and curled the ball off the post into the top corner.
Wellington snatched one back when Emma Pijnenburg whipped a ball into the box and Mackenzie Anthony forced a save from Mieres, but Woods tapped home the rebound.
From there, Mieres denied the Phoenix multiple times to preserve City's lead.
"It's really disappointing but our season was amazing and really proud of everyone," Phoenix skipper Mackenzie Barry told Network Ten.
"It's just a shame it had to end like that."
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