Wellington forward Maya McCutcheon's header in the second minute opened the scoring at Porirua Park, before Nickoletta Flannery responded off the bench in the 61st.
In the later games on Saturday, Central Coast drew 1-1 with Canberra United and Melbourne City defeated Newcastle 2-0.
Victory (29 points) sit ahead of third-placed Adelaide United on goal difference and seven points behind leaders Melbourne City.
Wellington (20 points), who had 17 shots to Victory's nine, are eighth after spurning a chance to jump into the top six.
Victory were flat early and the Phoenix drew first blood.
Annalie Longo floated a corner to the near post and McCutcheon made a wonderful run to flick home the opener.
Wellington's Manaia Elliott hit the side netting in the 18th minute, and Victory goalkeeper Courtney Newbon made a great save to deny the teenager in the 51st minute
Victory coach Jeff Hopkins turned to his substitutes on the hour mark, bringing on Holly Furphy and Flannery, and the move immediately paid off.
Furphy burst forward down the left and, after striker Emily Gielnik was unable to control her pass, Phoenix defender Tiana Jaber rushed a clearance and accidentally sent the ball straight to the feet of Flannery.
The winger burst down the right and smashed a wonderful strike into the far corner of the net.
Helped by Wellington's earlier draw, Canberra moved into the top six after salvaging a point against Central Coast.
The Mariners were on song first when Jade Pennock sidestepped defender Elizabeth Anton to hit the scoreboard in the 39th minute at McKellar Park.
It was the ever-reliable Michelle Heyman who struck back for Canberra less than 30 seconds into the second half after Maja Markovski outworked three defenders for the assist.
Taylor Ray sent in a long-range rocket on 87 minutes but her effort to restore the lead was denied by the post.
The home side were controversially denied a penalty in the final minute of regulation time when Aideene Keane was pushed to ground by Mariners defender Annabel Martin in the box.
Central Coast keeper Sarah Langman quickly swept up the ball and resumed play, before Canberra's Hayley Taylor-Young tried to find the back of the net but hit the post instead.
At McDonald Jones Stadium, Newcastle walked away with no reward for effort on the scoreboard.
Despite the home side taking 20 shots to 12, it was City who claimed the three points thanks to Laura Hughes's 69th-minute goal and a 84th-minute strike by Holly McNamara.
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