The international match against Iceland was Japan's last scheduled match before Japan head to North America for the World Cup, where Sweden, among others, await in the group stage.
Japan had the upper hand in terms of play for much of the match, but it took until the 87th minute before the team was able to break the deadlock.
Substitute Koki Ogawa, who plays for Nijmegen in the Netherlands, scored the winning goal after an assist from Werder Bremen's Yukinari Sugawara.
Sweden and Japan will meet on June 26 in the final group match for the teams. The Netherlands and Tunisia are also in the group.
This summer's World Cup in the United States, Canada and Mexico runs from June 11 to July 19.
