Aya Miyama gave Nadeshiko Japan the lead shortly before halftime at Komaba Stadium and Ono doubled the advantage with what proved to be the clincher on 58 minutes.
Substitute Caitlin Campbell grabbed a late consolation for New Zealand with a free kick deep into injury time.
The match was serving part of Japan's buildup to the Women's Asian Cup in China next May. Asia's flagship women's tournament doubles as a qualifier for the 2011 Women's World Cup in Germany.