The Samurai Blue bowed out of the tournament in Brazil after losing to Cote d'Ivoire and Colombia either side of a dour draw with Greece
The Samurai Blue kicked off their campaign with a 2-1 loss to Cote d'Ivoire and, after being held to a frustrating 0-0 draw by Greece, went into their final Group C fixture needing to defeat Colombia to have any chance of progressing to the last 16.
However, Japan were routed 4-1 by the South Americans, prompting Zaccheroni to call time on his four-year spell with the Asian nation.
"I feel disappointed and unsatisfied with our results," the Italian coach told reporters on Wednesday.
"We were confident and enthusiastic about getting through the group stage before the tournament.
"It's only a short period of time, but we stumbled in the beginning of these three matches and didn't play as we'd imagined.
"And just as it's been for the last four years, the results came from the players and tactics that I selected, so the responsibility lies completely with me. I want to take responsibility.
"At lunch the entire team gathered together, and I thanked the players, staff, JFA (Japan Football Association) officials, and everyone else who has supported us for the last four years.
"I feel that now is time for me to leave the Japan national team. A new manager will fill up what's missing and make this team even stronger."