The Mexican replaces Zaccheroni as boss, after the Italian resigned at the conclusion of Japan's disappointing World Cup campaign.
After exiting the finals in Brazil with just one point from group matches against Ivory Coast, Greece and Colombia, Zaccheroni left his post, with the 56-year-old Aguirre confirmed as his successor on Thursday.
"Japan Football Association has decided that the new coach of the Samurai Blue will be Javier Aguirre," a statement on the Japanese FA's official website read.
Aguirre has previously had two spells in charge of the Mexico national team, overseeing their World Cup campaigns in both 2002 and 2010.
In May, Aguirre left his role as head coach of Espanyol after a 14th-place finish in La Liga in his only full season in charge at the club.