The Group B leaders surrendered a one-goal lead against the 10-man Socceroos, but the Italian was pleased with the performance away from home
The Samurai Blue took the lead thanks to Yuzo Kurihara's close-range goal, but surrendered the equaliser just three minutes later following a questionable penalty kick awarded to the hosts which was duly converted by Luke Wilkshire.
The hosts were already down to 10 men after Mark Milligan was shown a second yellow card for a foul on Atsuto Uchida, but the Italian coach was pleased with his side's performance.
"Australia played to win and fought with their physicality, experience and cunning," Zaccheroni said after the match. "But we didn't let ourselves be defeated by that and fought back just as hard.
"We had a difficult start but we overcame that and gained control of the match. For an away game Japan played magnificently."
Playmaker Keisuke Honda, who crossed for Kurihara's goal, was satisfied with the result despite personally failing to score in a third straight World Cup qualifier.
"Of course we wanted to win, but a 1-1 away result isn't bad at all," the CSKA Moscow attacker reflected. "All we can do is take it as a good result and think ahead to the next match."
Goalkeeper Eiji Kawashima, who prevented several Socceroo goals with superb saves throughout the match, praised his team-mates for standing up to their physical opponents.
"We knew that they would attack with long balls and crosses, but each one of us put our bodies on the line and stopped them," the 29-year-old told reporters.
Japan continue to lead Group B with seven points from three games, while Australia have just two points from two matches. The sides will next play on September 11, when Japan host Iraq and Australia travel to Jordan.