Nisbet polled 36 votes ahead of Melbourne Victory striker Bruno Fornaroli (29) and Wellington Phoenix's Kosta Barbarouses (28).
The 24-year-old Mariners midfielder notched three goals and nine assists across the regular season, with his form leading to his first Socceroos cap in March.
Nisbet was presented the award after the Mariners' 3-1 grand final win over Melbourne Victory on Saturday at Industree Group Stadium.
"Josh is an incredible talent and continues to get better each year," said A-Leagues commissioner Nick Garcia.
"An academy product who has now played over 120 games, Josh is a great role model for other young players coming through the league and for fans alike with his professionalism, hard work and dedication to always try and improve."
Nisbet celebrating a Miguel Di Pizio goal in the grand final. (Dan Himbrechts/AAP PHOTOS)
Nisbet is the Mariners' first Johnny Warren Medal winner and his gong came after the vote for the league's young footballer award was split for the first time.
Wellington goalkeeper Alex Paulsen and Adelaide's Bayern Munich-bound winger Nestory Irankunda shared the award.
Paulsen, 21, was also named goalkeeper of the year after his breakout season in which he conceded just 26 goals, the least of any keeper in the home-and-away series.
Central Coast boss Mark Jackson claimed the coach of the year award.
Under the first-year coach, the Mariners turned around their 0-4 start to the 2023/24 campaign to win the premiers' plate, claim back-to-back championships and become the first Australian club to win the AFC Cup.
2023-24 JOHNNY WARREN MEDAL ROLL OF HONOUR:
*Johnny Warren Medal: Josh Nisbet (Central Coast Mariners).
*Young footballer of the year: Nestory Irankunda (Adelaide United)/Alex Paulsen (Wellington Phoenix)
*Coach of the year: Mark Jackson (Central Coast Mariners)
*Golden Boot: Adam Taggart (Perth Glory)
*Golden Glove: Alex Paulsen (Wellington Phoenix)
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