Kudo was in intensive care after brain surgery in Japan this week, but died on Friday.
The striker made 14 appearances for the Roar in the 2020-21 A-League Men season, scoring one goal.
"I like everyone else at Brisbane Roar I am deeply saddened by the news overnight that our former teammate, player and friend Masato Kudo has passed away," Roar coach Warren Moon said in a statement.
"He had such a wonderful personality and always turned up to training every morning with a beaming smile on his face.
"He will be greatly missed, and our hearts go out to his wife and young daughter at this sad time."
The Roar confirmed they would be wearing black armbands to honour Kudo in Saturday's game against Western Sydney Wanderers.
Kudo made four senior appearances for Japan, scoring two goals.
Along with his ALM stint, Kudo spent 2016 in the MLS with Vancouver Whitecaps but otherwise spent the majority of his career in Japan.
Kudo started at Kashiwa Reysol and also had stints at Sanfrecce Hiroshima and Renofa Yamaguchi, while he most recently played for third-tier outfit Tegevajaro Miyazaki.
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