The Mexican took charge of his new side for the first time against Uruguay on Friday but the landmark occasion ended in disappointment.
Goals in each half from Edinson Cavani and Abel Hernandez sealed a 2-0 success for the visitors in Sapporo and Aguirre will be hopeful of a different outcome in Yokohama this time around.
The former Espanyol boss, in his third spell of international management after two stints with Mexico, remained upbeat following the loss to Uruguay.
"We need to keep working a lot more," he said.
"We have our next match against Venezuela on Tuesday, so we want to keep our head up."
Tatsuya Sakai made his international debut in Sapporo and the Sagan Tosu defender is eager to feature more for his country.
"It was a first international appearance for me and I realised there were some things I could do and some things I couldn't," he said.
"I was very excited to play in front of the full crowd and found it a good atmosphere, I definitely want to play longer."
Ranked 29th in the world, Venezuela fell short of World Cup qualification in the South American section, ending the campaign five points behind Uruguay, who took the intercontinental play-off berth.
Japan did manage to reach the finals in Brazil but under Alberto Zaccheroni they failed to a win a game, taking just one point from group fixtures against Ivory Coast, Greece and Colombia.
Like Japan, the visitors are also under new management following the appointment of Noel Sanvicente in July.
As with Aguirre, Sanvicente's first match in charge ended in defeat as his side suffered a 3-1 reverse against South Korea in Bucheon on Friday, despite taking the lead through Mario Rondon.
"In a short time, we have reviewed the tactical aspects," Sanvicente said.
"We have another test in Japan who are classy, but with different characteristics [to South Korea]."
Sanvicente will be unable to call upon the services of star striker Salomon Rondon, who was sent off late on against South Korea and will now serve a suspension.
