Messi, 31, was the runner-up in 2007 and 2008 before winning for the first time in 2009.
The manager also revealed that he did not speak to Ronaldo before the Portuguese moved on.
The Fifa World Cup in Russian Federation provides several of the goals on the shortlist.
While his worldwide team-mates geared up for games against Croatia and Italy, Ronaldo was put through his paces alongside Sami Khedira, who was left out of the recent Germany squad after a disappointing World Cup.
He's joined by English Premier League top scorer and player of the year Mohamed Salah, who is nominated for his derby day goal against Everton, and former Real Madrid teammate Gareth Bale, whose own Uefa Champions League overhead kick makes the list. However, former Real Madrid boss Zinedine Zidane has set the record straight.
France's World Cup winning squad players also missed out on a place in the top three finalists.
France's World Cup winning captain Hugo Lloris is in contention for the goalkeeper of the year award, alongside Golden Glove victor Thibaut Courtois and Danish shot-stopper Kasper Schmeichel.
Messi has won four Champions League titles to Ronaldo's five although the Argentine's last win came back in 2015.
The main thought behind wanting Messi to be recognised was not just the fact that he had another stellar campaign individually (45 goals in 54 games), but that Barcelona won three trophies (La Liga, Copa Del Rey and the Spanish Supercup).