"The two matches will be very important for us as a great opportunity to prepare for [Asian] World Cup qualifiers starting in September," Japan coach Alberto Zaccheroni said in a statement released by the association.
"I hope all our national team players will take good advantage of this opportunity to understand each other better," the former AC Milan coach said.
The two visiting sides will play each other on 4 June in Nagano in an annual three-nation tournament called the Kirin Cup.
The disasters forced the cancellation of home friendlies against Montenegro and New Zealand in March and led the nation's J.League to suspend five rounds of matches.
The backlogged league fixtures will be played in July to clash with the Copa America, to which Japan are invited as guests.
Reversing an earlier decision to withdraw from the Copa America, Japan pledged to take part in the event by selecting a squad mainly made up of European-based players.