The Schalke man converted Shinji Kagawa's blocked effort as Albert Zaccheroni's men got off to a laboured start in their preparations for the World Cup
Alberto Zaccheroni's side have now won three friendlies in a row but showed little sign of the quality that helped them recently overcome Belgium and New Zealand on Tuesday.
While Japan enjoyed the better of the first-half possession, they were forced to wait until two minutes before the break for Atsuto Uchida to open the scoring.
After good work from Shinji Kagawa, Uchida finished from close range at the second attempt but the scoring ended there, despite their dominance after the interval.
Yoichiro Kakitani, Kagawa and Yoshito Okubo all went close but to no avail against a stubborn Cypriot defence - leaving Zaccheroni with plenty to ponder ahead of meetings with Costa Rica and Zambia as well as their Group C opener against Cote d'Ivoire.
Japan named a strong side that included Kagawa, Keisuke Honda and Shinji Okazaki but it was Cyprus who started the brighter.
Aside from an early corner, Pambos Christodoulou's men failed to test Japan sufficiently, however, as the home side grew into the game - Honda's shot saved well after good link-up play with Kakitani.
The pair combined again shortly after, Kakitani almost getting on the end of Honda's delivery, before Uchida struck the ultimate winner.
After Kagawa crafted a chance on goal with a clever flick, he was denied by an Angelos Charalambous tackle, with Uchida's follow-up blocked.
However, the Schalke defender showed persistence to tap home the loose ball.
It was one of Uchida's final contributions as he, Yasuhito Endo and Yasuyuki Konno made way for Hiroki Sakai, Maya Yoshida and Makoto Hasebe at the break.
Japan almost doubled their advantage when Giorgos Merkis gave the ball away to Kagawa who slipped in Kakitani. However, Panos Constantinou saved well, with Kagawa unable to reach the loose ball.
Kagawa again forced a strong save from Constantinou before Kakitani was replaced by surprise squad inclusion Okubo but the in-form Kawasaki Frontale striker saw his first effort deflected wide.
After large spells of dominance from the home side, Onisiforos Roushias could have secured a late equaliser had he kept his cool when played in on goal rather than blasting an effort into the side-netting.