The 28-year-old, whose fine performances saw him signed by English Premier League club Aston Villa from Dutch side AZ Alkmaar for next season, beat out Japan-based Alex Brosque and Reading goalkeeper Adam Federici.
"Brett Holman was a standout player for both his club, AZ Alkmaar, and the Socceroos in the past year," said PFA president Simon Colosimo.
Previous winners of the PFA player of the year award since its introduction in 2009 have been Tim Cahill, Mark Schwarzer and Matt McKay. Canberra United goalkeeper Lydia Williams was named the best female player. The PFA was established in 1993 as the representative body of Australia's professional footballers.