Thailand had only 14 players available for the last-eight match in India after Covid-19 swept through the squad.
The depleted Thais fought bravely but Japan slowly took control of the match, clinching a semi-final berth powered by Yuika Sugasawa’s hat-trick.
However, Thailand can still qualify for the 2023 FIFA Women's World Cup via the play-offs.
The Thai women play Vietnam on Wednesday followed by Taiwan on Friday. If they win both those games, Thailand will book their berth in next year’s World Cup in Australia and New Zealand. If not, they will have to qualify via inter-confederation play-offs.