Staring down the barrel of an upset defeat after Francisco 'Chico' Geraldes' first A-League goal had restored the hosts' lead at Sky Stadium, Milanovic received a pass from Brandon Borrello, cut inside and laced a ball into the top corner.
The 23-year-old, one of the most notable omissions from Australia's squad for recent World Cup qualifiers, pressed his case for a call-up with the pressure-laden equaliser.
Milanovic picked up right where he left off in the first game since the international break, celebrating his fourth goal in as many games and tenth of the campaign.
It salvaged a point that ensured Alen Stajcic's unit extended their unbeaten run to seven games.
The Wanderers are now within three points of second-placed Western United, both sides having now played 21 games.
But the draw also snapped a four-game winning run, leaving Western Sydney vulnerable to falling to fifth if results elsewhere go against them.
"We've been in really good form over the last five or six weeks," skipper Lawrence Thomas told Sky Sport NZ.
"We're aiming quite high; the goal was three points.
"But in saying that, at least we didn't lose, so we take the point back."
Expected to make light work of a Wellington side that hadn't won since January, the visitors fell behind in the 21st minute.
Goalkeeper Thomas found his path to contest a Hideki Ishige corner blocked by a tussle between Kazuki Nagasawa and Jack Clisby, opening up space for Corban Piper to attack the ball in flight.
Parity was restored 15 minutes later when Milanovic found space and cut the ball back for Bozhidar Kraev, producing his sixth assist of the season.
But the Phoenix responded and re-took the lead when Geraldes buried a shot into the bottom corner in the 69th minute.
Playing for pride after drawing a line through their finals hopes, Giancarlo Italiano's side appeared destined for just their second home win of the season, only for Milanovic to pop up late and break Kiwi hearts.
"I was disappointed that we couldn't close the game out," Phoenix coach Italiano admitted to Sky Sport NZ.
"When your form is against you a little bit, sometimes you forget how to win.
"It felt like that, especially for the last 15 minutes."
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