Longo announced her return from injury by opening the scoring in the 35th minute before clinching the match-winner in the 69th at Porirua Park.
Also on Sunday, Western United claimed a 2-1 win over reigning champions Sydney FC, who sit a lowly 11th, while Adelaide defeated Newcastle 2-0.
Wellington edges closer to the top-six after securing their second win of the season against a Brisbane Roar outfit without star Matilda midfielder Tameka Yallop and winger Sharn Freier.
The Phoenix are eighth (2-3), while the Roar (3-2) remain second on the table.
Longo intercepted a poor pass from Roar defender Leia Varley meant for Holly McQueen before pulling off a one-two with teammate Olivia Fergusson to find her first goal.
Emily Pringle scored the Roar's goal in first half injury time to make it 1-1. (Darren England/AAP PHOTOS)
Roar equalised a minute into added time before the break when 'Nix midfielder Daisy Brazendale mistakenly released to Emily Pringle, but Longo popped up again in the second half to complete her double.
Longo had been out of action since round three after suffering a gruesome facial injury against Newcastle.
Roar striker Evdokiya Popadiynova is set for a stint on the sidelines after suffering a hamstring injury while chasing down Phoenix centre-back Mackenzie Barry in the 54th minute.
At Ironbark Fields, substitute Kiara de Domizio scored in the 89th minute against Sydney to gift Western United the three points.
The hosts found a way through the stalemate in the 55th minute when Kahli Johnson launched a long-range left-footed shot.
But their elation did not last long, with Sky Blues substitute Amber Luchtmeijer equalising three minutes later.
Western United began the more daring side in the second half and found their reward through de Domizio.
Adelaide star Fiona Worts put on a show at ServiceFM Stadium, scoring in the 45th and 63rd minute to lift her side to third on the table in a 2-0 win over Newcastle.
The Reds' first goal arrived after Newcastle goalkeeper Danielle Krzyzaniak, handled the ball outside the area.
She then spilled Emily Condon's free kick and in a goalmouth scramble, Worts eventually forced the ball over the line.
Eighteen minutes later, Worts tapped home a lovely ball from Lucia Leon.
Perth host Melbourne Victory in the late game at the Sam Kerr Football Centre.
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