The NZ outfit finally registered their first success of the 2013-14 campaign, accounting for the Sky Blues to take a long overdue three points at the 'Cake Tin'
Questionable defending from Sydney FC allowed Wellington to feast on several opportunities in the first half and they took a deserved 1-0 lead at the break.
Despite the defensive frailties at the back from the visitors it was a piece of attacking brilliance from Carlos Hernandez that led to a relieved Stein Huysegems scoring the opener after 33 minutes.
The second half started badly for the hosts when Paul Ifill needed to be stretchered off the field with an Achilles injury.
But Sydney were still unable to find a precious goal as the Phoenix held on for their first victory of the season in front of 6,339 fans in Wellington.
The win is the first under coach Ernie Merrick and it moved the Phoenix up to 10 points.
As for Sydney FC, who entered the match with five wins from their past six matches, their attacking mojo was severely deflated with the absence of injured Italian star Alessandro Del Piero.
Coach Frank Farina, however, will be more concerned about the generous defence that gifted plenty of chances for the hosts.
The Phoenix dominated the opening half and were deservedly up 1-0 at half-time courtesy of Huysegems' third goal of the season.
The relief was noticeable for the former Belgium international, who missed a crucial penalty against Central Coast on Thursday that ultimately denied his team a point.
After taking a superb ball from Hernandez, rounding goalkeeper Vedran Janjetovic and passing into the net from a tight angle, Huysegems ran to fellow striker Jeremy Brockie and the rest of the bench to celebrate.
At the other end, Joel Chianese added his name to the Westpac Stadium wall of shame after his slipped shot in front of a vacant goal crawled wide to the delight of the Yellow Fever.
Ali Abbas then tested Glen Moss but the comfortable height ensured the New Zealand shot-stopper was always in control.
The only thing more in control than the Phoenix's defence was their attack.
A superb piece of work from Ifill found Huysegems in the middle of the box, but his effort hit the post before he miskicked an attempt minutes later.
The 31-year-old striker then looked to have been felled in the penalty area only for referee Peter O'Leary to wave play on.
It was Huysegems' goal that separated the two teams at half-time.
Ifill was stretchered off early in the second half before Ranko Despotovic's effort limped over the bar.
Hernandez had a fantastic opportunity to double the Phoenix's lead with 25 minutes to play but his effort was well saved by Janjetovic from close range as the hosts maintained their intensity in attack.
The visitors looked naive going forward and were left to rue giving away possession in the final third as the minutes ticked down.
They had few chances but were threatening on the counter-attack.
Huysegems had a chance to seal the match with two minutes left to play but his shot soared well over the goal to ensure a thrilling final few minutes, but Merrick's men held on.
Wellington Phoenix 1 (Stein Huysegems 33)
Sydney FC 0
Crowd: 6,339 at Westpac Stadium