Vïctor Sánchez made his return to the starting eleven after missing the last two games with a hamstring injury.
United was otherwise unchanged.
Bradden Inman made the match day squad for the first time since signing with the club.
Lachie Wales copped a nasty knock and fall in the early stages and looked almost certain to be subbed off with a head injury.
Wales was quickly assessed and was deemed okay to continue, however.
The 23-year-old won a penalty for his side soon after when he was brought down by Wellington’s Tim Payne.
Besart Berisha tucked the penalty away in the bottom-left corner for his seventh goal of the season.
Phoenix was awarded a spot-kick themselves minutes from the half-time break after United defender Andrew Durante was penalised for handball.
Ulises Dávila sent Ryan Scott the wrong way to level the score going into the break.
The goals continued in the early stages of the second half for both sides.
Josh Sotiro got a slight touch on a Dávila strike, which wrong-footed Ryan Scott before finding its way into the back of the net.
Phoenix's lead lasted some two minutes however, as United’s Iker Guarrotxena nabbed his second goal of the season.
Andrew Durante’s strike rattled the crossbar before Guarrotxena headed home the follow-up.
Kaine Sheppard had the best chance for United from thereon but couldn’t generate enough power in his header to trouble Phoenix keeper Oliver Sail.
The Phoenix snatched the win in the 90th minute through Ben Waine, whose header looped into the top corner.
What Mark Rudan said
"We knew it was going to be a tough game tonight but there’s one thing having games in hand but you’ve actually got to pick up points at the same time.
"We’ve got a few new faces this week that have only just joined and I’m sure with a huge amount of games coming up in the next month that there will be a lot of opportunities for a lot of players.
"Nothing changes as far as we are concerned. We keep the messages positive as well.
"The boys are down, that’s natural, we lost the game last minute. But we’ve got to pick them up quickly and keep the messages positive."
Western United will travel to Launceston, Tasmania to take on Central Coast Mariners on Saturday, 17 April. Kick-off is 5:05pm at UTAS Stadium.