The Italian's team were fancied to have an impact in Brazil but failed, finishing winless and bottom of a group, which included Colombia, Greece and the Ivory Coast.
Former Juventus, Inter, Lazio and Milan coach Zaccheroni, 61, took responsibility and resigned.
In an open letter on the Japanese Football Association's (JFA) website on Thursday, Zaccheroni said there was "loneliness and frustration" but he feels he leaves the country in a good place.
"The frustration has still continued but there is one thing to save me from it," he said.
"It is the certitude that I had managed to form a group for the future. I can say that on both the football style and the age structure of the team.
"Most players who played in this World Cup should be able to play in the next one as well. JFA also told me that they are going to be based on what we had built and brush it up even more."
Zaccheroni said he was proud of what he had achieved in his four years in charge, including winning the 2011 AFC Asian Cup and 2013 EAFF East Asian Cup.
The veteran coach had a message for Japan, saying they needed to have belief when they head to Russia in 2018.
"If I am allowed to leave a message for the next team, I would say that it is important to be able to show the strong feeling of 'we are going to do it' and 'we are going to be the leading part in World Cup' more than before," Zaccheroni said.
"For the next World Cup in Russia, I heartily hope them to achieve the further development by brushing up the style, cultivating the real confident with the ambition to be the main cast of football in the world.
"The way Japan football should go for is not to pursue the result only but playing better than opponents and also achieve a result. I believe that it is the way Japan pursue."