The Italian could not rouse his players following their 4-3 defeat on Thursday, meaning that they have finished bottom of Group A.
Despite not being able to win a match, Zaccheroni believes that the Confederations Cup has been a positive for his team.
"Mexico were fitter than us and controlled possession better," the 60-year-old told reporters. "Our game against Italy was exhausting, which is why we weren't as good today.
"The tournament has helped us to gain more international experience, which was something we were lacking, so overall we can look back positively on our time here."
Japan have already qualified for next year's World Cup.