In the group stage, India had defeated the Netherlands and Tahiti by identical margins of 5-0 before losing to formidable China 1-4.
Only Satwiksairaj Rankireddy and Chirag Shetty could manage a win in the tie as they beat He Ji Ting and Zhou Hao Dong 21-14 21-14.
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).
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.
The Thomas Cup and Uber Cup are now under a cloud of uncertainty after the Badminton World Federation confirmed that five countries have pulled out.
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.