The new three-year contract extension will keep the highly-rated full-back with the Nerazzurri until the summer of 2019.
“I never thought of leaving. As I said before, I love Inter and I want to give my all for our goal,” he told the club’s website.
“I’ve been here for five years and I’m happy, everyone treats me well.
“I feel at home. I want to thank the president, the club, [vice-president] Javier Zanetti, Roberto Mancini, the staff and the fans.”
Nagatomo claimed in January that he had turned down the chance to join Premier League giants Manchester United.