The Iranians will now bid for a stunning 10th Asian title when they tackle hosts Uzbekistan on Sunday in a repeat of the 2001 final, which ended in the former's favour.
Masoud Daneshvar opened the scoring against Japan after just one minute before adding a second 11 minutes later but that proved to be the last goal before the break.
Needing to claw back the two-goal deficit Japan went on the offensive after the restart and Iran took full advantage of the gaps in defence with Javad Asgharimoghaddam scoring a hat-trick and Mostafa Tayyebi and Mohammad Keshavarz Nasrabadi also getting on the score-sheet.
Five of the last seven AFC Futsal Championship finals have seen Iran tackle Japan and on each occasion the Iranians came out on top.
“This game was not the first time we have met the Japanese team so we knew all about their strengths and weaknesses,” he said.
“When we scored our second goal I realised that our rivals would put all their players outfield and that enabled us to go on and get such a great result.”
Defeated coach Miguel Rodrigo believes to beat Iran at the moment is almost impossible and conceded they were better than his side in almost every department.
The Japanese had been impressive in their run to the semi-finals with fourth successive victories during which they scored 20 goals and conceded just two.
But they were ultimately outclassed by Iran and Rodrigo had no qualms with the result.
“Iran have once again confirmed their status and to fight against them is practically impossible," he said.
“We tried to play well in this game but Iran were extremely good at making the most of their chances. The Iranians were stronger than us and showed their class and physical ability.”