Alex Chidiac, meanwhile, scooped the Julie Dolan Medal for best women's player for the second time in her career.
Matildas midfielder Chidiac follows just four other players - Michelle Heyman, Sam Kerr, Clare Polkinghorne and Taryn Rockall - in winning the award twice after helping club side Melbourne Victory reach the A-League Women grand final.
Milanovic, was in influential touch for the Wanderers, banging in 12 goals that earned him a call-up to the Socceroos training camp and a move to Scottish side Aberdeen.
"It's amazing for our club and Nicolas who has had a wonderful couple of years," said Wanderers chief executive Scott Hudson.
"The club is really proud of his achievements, he grew up in Western Sydney and sat in the RBB as a young kid.
"To see him win this accolade and sit alongside some of the greatest names that have played our game, we're super proud of him."
Adelaide's Archie Goodwin claimed the young player-of-the-year award and split the ALM golden boot with Sydney playmaker Adrian Segecic.
Steve Corica was named best coach after helping Auckland claim the premiership in their maiden season in the competition.
Chidiac, though, said she wished she could swap her individual gong for the grand final trophy which eluded Victory after they lost to the Central Coast Mariners in a penalty shootout.
"It's a weird one, I don't deal well with personal awards but it is an honour," Chidiac said.
"I'm still not done yet, I'm hoping for a third."
Adrian Stenta was named coach of the year after taking Adelaide from bottom to third on the table and winning their first-ever finals match.
Melbourne City's Holly McNamara claimed the golden boot with 15 goals in 17 games, while Indiana Dos Santos of Sydney FC scooped the young player prize.
2024-25 DOLAN WARREN AWARDS ROLL OF HONOUR:
A-LEAGUE MEN
*Player of the year: Nicolas Milanovic (Western Sydney)
*Young player of the year: Archie Goodwin (Adelaide)
* Coach of the year: Steve Corica (Auckland)
* Golden boot: Adrian Segecic (Sydney FC) and Archie Goodwin (Adelaide) - 13 goals
A-LEAGUE WOMEN
*Player of the year: Alex Chidiac (Melbourne Victory)
*Young player of the year: Indiana Dos Santos (Sydney FC)
* Coach of the year: Adrian Stenta (Adelaide)
* Golden boot: Holly McNamara (Melbourne City) - 15 goals
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