The cobwebs showed as the Blue Samurai struggled to penetrate a spirited Peru side in their first official game since March's deadly earthquake and tsunami.
The South Americans hit the post twice late on in rain-swept Niigata after Japan substitute Ryota Moriwaki had almost put through his own goal in the 83rd minute.
Japan goalkeeper Eiji Kawashima tipped a volley from striker Raul Ruidiaz against the post before Luiz Ramirez's header came back off the post seconds later.
The home side came closest to scoring when substitute Keisuke Honda blazed a free-kick just over 10 minutes into the second half in front of 39,000 at Big Swan World Cup stadium.
Japan's Italian coach Alberto Zaccheroni did at least have the consolation of seeing his side stretch their unbeaten home run under his charge to a record 13.
Peru take on the Czech Republic in the next game of the three-nation Kirin Cup in Nagano on Saturday before Japan face the Czechs in Yokohama on June 7.
Montenegro and New Zealand both pulled the plug on friendlies in Japan at the end of March citing the potential risk posed by the nuclear crisis raging north of Tokyo.
