Messi, 32, lifted a record sixth Golden Ball at the prestigious awards gala in Paris on Monday, beating Virgil van Dijk by a slender seven votes.
And the Argentina captain, who ranked the Dutchman's Liverpool teammate, Mane, as the best player in the world for the 2019 FIFA Best Men's award, questioned his podium snub in France.
"It's a shame to see Mane finish in fourth place," Messi told Canal+ Sport Africa. "But I think there have been a lot of great players this year.
"That's why it was difficult to choose a particular player. But I chose Sadio Mane (for The Best award) because he's a player that I like.
"Mane achieved a great year that was exceptional for the entire Liverpool team. That's why I chose him. I repeat, there were a lot of very great players this year, so the choice was difficult."