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World No. 7 Sindhu was off colour for the second consecutive day as she squandered a game lead to go down 21-18, 17-21, 12-21 to Intanon, ranked eighth, in a 59-minute first women's singles match.
The Indian women humbled USA 4-1 to notch up their second successive win in Group D.
No replacement could be named for Gayatri since the extent of her injury came to light after the deadline for making any change to the squad was over.
Competing without Olympic medallist P V Sindhu and hampered by the injury-forced ouster of Saina Nehwal, the Indian women lost 0-3.
The women's team had already reached the quarterfinals. However, it was their first defeat in the event after beating Spain (3-2) and Scotland (4-1).
India scored a convincing 4-1 victory over Scotland.
Indian women produced a clinical display to notch up a 3-2 win over Spain in the Uber Cup.
The tournament, slated to be held in Denmark from October 3 to 11, was set to mark the resumption of international badminton after it came to a halt in March following the outbreak of the novel coronavirus.
Sindhu changed her original decision to pull out of the event due to personal reasons after Badminton Association of India President Himanta Biswa Sarma requested her to play.
The world champion could also miss the subsequent Super 750 tournaments in Denmark due to personal reasons.