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The second seed Indo-Australian pair lost 5-7, 6-2, 2-6.
They beat last year's finalists Sander Gille and Joran Vliegen in three sets.
The 44-year-old Bopanna wrote to the AITA and also marked TOPS in the mail, conveying his decision - a development confirmed by the national federation.
The World No 1 defeated the Argentine 6-1 5-7 3-6 7-5 6-3 to reach the quarterfinals.
The Brazilians made life tough for the Australian Open champions who scraped through in two hours and seven minutes.
The two had an interaction during the Manorama Sports Awards 2023 ceremony in Kochi on Tuesday.
Bopanna and Ebden rallied to down Ivan Dodig and Austin Krajicek 6-7(3), 6-3, 10-6 in a hard-fought final.
Bopanna also became only the third Indian to win a men's doubles Grand Slam title.
Bopanna and his Australian partner Matthew Ebden prevailied in a tense semifinal against Tomas Machac and Zhang Zhizhen.
The second-seeded Indo-Australian pair will cross swords with unseeded Tomas Machac and Zhizhen Zhang in the semi-finals.