Norway forward Erling Haaland, 23, scored 52 goals in all competitions in his debut season with Pep Guardiola's side.
Haaland beat team-mates Kevin de Bruyne and John Stones, Arsenal's Saka and Martin Odegaard and Tottenham's Harry Kane, now at Bayern Munich.
City won the Premier League, FA Cup and Champions League last season.
Erling Haaland joined City from Borussia Dortmund in a deal worth £51.2m in June 2022.
He was also nominated for the young player prize, which was awarded to England winger Saka after he scored 14 goals and contributed 11 assists in his finest season for the Gunners.
The 21-year-old beat fellow nominees Moises Caicedo, who recently joined Chelsea from Brighton, Aston Villa midfielder Jacob Ramsey, Arsenal forward Gabriel Martinelli and Brighton striker Evan Ferguson.
Meanwhile, both winners of the individual prizes were also included in the PFA Team of the Year.
Aston Villa striker Rachel Daly won the PFA women's Player of the Year award, while Chelsea's Lauren James was named Young Player of the Year.
Despite being eligible and on the shortlist, Haaland failed to win the award for Young Player of the Year; that award went to Arsenal star Bukayo Saka. However, winning the main prize means that City have now claimed it three times in the last four years after Kevin De Bruyne's double in 2020 and 2021.
The dominance of the Blues was also seen in the PFA Team of the Year, which was filled with no less than five City stars from their title- and Treble-winning team. Alongside Haaland, De Bruyne made it in as well as Ruben Dias, Rodri, and John Stones.
PFA Team of the Year: Aaron Ramsdale (Arsenal), William Saliba (Arsenal), Ruben Dias (Man City), John Stones (Man City), Kieran Trippier (Newcastle), Rodri (Man City), Martin Odegaard (Arsenal), Kevin de Bruyne (Man City), Bukayo Saka (Arsenal), Harry Kane (Tottenham), Erling Haaland (Arsenal).