Cristiano Ronaldo, Luka Modric and Mohamed Salah made the cut ahead of the Argentina captain, who fired Barcelona to a domestic double last season.
Peter Schmeichel tipped Modric, the World Cup Golden Ball winner, to win the award at the unveiling of the nominations in London.
“I think we have a new winner this year,” said the former Manchester United goalkeeper. “I think his performances were fantastic. Rightly so he got best player at the World Cup and I fully expect him to win this.”
Schmeichel’s son Kasper was shortlisted alongside Hugo Lloris and Thibaut Courtois for this year’s award for best goalkeeper.
Messi misses out on the final three for the overall player of the year for the first time since 2006. He was part of the initial top 10 nominees, with Kevin De Bruyne, Raphael Varane, Antoine Greizmann, Eden Hazard, Harry Kane and Kylian Mbappe joining him in failing to make the cut.
Ronaldo and Modric are rewarded for helping Real Madrid to a fourth Champions League title in five seasons, with the latter inspiring Croatia to a first World Cup final. Modric won best player at last week’s Champions League awards, which Ronaldo failed to attend.
Liverpool’s Salah scored 32 goals to pip Harry Kane to the Premier League golden boot, while he also led Egypt to a first World Cup appearance since 1990 before a shoulder injury prevented him from hitting peak form in Russia.