The win denied Japan a place in the final. The Japanese went into the match knowing that only a five-goal win will take them to the final against India.
But the Malaysians played a well-defended game and in one quick moment scored the winning goal which deflated the Japan side.
That goal came in the 58th minute of the match with Abdul Muhajir off a field attempt.
The Malaysians will play New Zealand in the play-off for fifth placing.
But Malaysian coach Nor Saiful Zaini said the result do not mean that they are an improved side.
“We still face a tough time whoever we play. We drew 5-5 with New Zealand in the group phase and held the lead for a long time. Still, we could not finish off the moves.
“There are still areas where we need to rectify and to make sure we do not make the same mistakes.
“As I have said earlier we are still learning and for some players this just their debut tournament. We will go all out t get a result, but we must also e realistic about our chances,” he said.
In the match against the Japanese, the Malaysians defence was a disciplined lot and managed to keep out the ball from the danger zone.
The Japanese grew impatient as their attacks fell flat and this allowed the Malaysians to capitalise and keep them at bay.
Japanese coach Hiroki Sakamoto was disappointed with the players showing.
“I think we could have done better. We missed some easy chances and that hurt us. I am happy with the overall play of the team. But we need to improve on our game plan.
“So we will now try and get a result against Australia and hope to finish in third place,” he said.