In a match they had to win, Malaysia trailed 1-2 as the clock was ticking away.
But a sterling finish by man of the match Amirul Azhar turned the tables as the Malaysian team played its best match in the tournament thus far.
It was Malaysia that opened scoring in the 5th minute through Muhamad Zainuddin.
But Japan nudged to a 2-1 lead via goals from Sota Ukai ( 8th minute) and Ryuji Tamekuni (12th minute).
However in the third quarter Malaysia drew level via a penalty corner by Amirul Azhar in the 42nd and 50th minutes.
Japan were unlucky not to have got an equaliser in the dying minutes, but their inability to put away chances cost them a point at the very least.
Perhaps it was the fact that India and Great Britain had drawn their earlier match that deflated the Japanese who lost all hopes of making the final.