German-based striker Yuki Ogimi scored the winner seven minutes into the second half in mountainous Nagano as the home side finally broke through after a frustrating start.
It was the Wolfsburg player's 53rd goal in 117 games for her country.
“We know it won't be easy to retain the World Cup but that's our ultimate aim,” Japan coach Norio Sasaki told reporters.
“It will be a tough ask but we will give everything to lift the trophy again.”
Japan, who will be favourites to top a group also involving Switzerland, Cameroon and Ecuador, produced an astonishing upset to win the World Cup four years ago, beating the mighty United States in the final.
Sasaki's side added last year's Asian Cup title after settling for silver at the 2012 London Olympics, where the Americans took revenge for their defeat in Frankfurt. The World Cup kicks off on June 6th.