The 30-year-old ended a five-year stint at Wolfsburg to join Nuremberg last season, but was restricted to just 14 Bundesliga appearances due to a serious knee injury.
Nuremberg were eventually relegated and Frankfurt - who recently appointed Thomas Schaaf as head coach - have swooped to sign the Japan captain.
"We are pleased that we were able to sign an experienced player who has shown over the past few years his skills in the Bundesliga," Hubner told Frankfurt's official website.
"We wish him much success in the World Cup in Brazil and that he will lead (his team) as far as possible."
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