Chile, scoreless in this tournament before the Thailand match, needed to win by three goals to advance as a third-place team.
Chile was ahead 2-0 when it was awarded a penalty in stoppage time after video review showed Thailand goalkeeper Waraporn Boonsing had committed a foul just before Maria Jose Urrutia's was cleared off the line by Natthakarn Chinwong.
The kick failed when Francisca Lara hit the crossbar.
Urrutia's header 10 minutes before the end of regulation gave Chile a chance at qualifying for the knockout stage in its first World Cup appearance.
Urrutia was player of the match.
Chile and Thailand were both eliminated.
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