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The Mallorcan, who played on four Davis Cup-winning teams for Spain, was tearful as the national anthem was played before the tie.
The 38-year-old Spaniard has won 22 Grand Slam titles.
The Spaniard's career has been hampered by injuries. He missed the 2023 French Open and was beaten in the first round this year.
24 Grand Slam winner Djokovic is chasing his maiden Olympic gold.
However, the Nadal I saw at the media centre was entirely different. He looked calm and friendly.
Nadal missed almost all of 2023 with a hip problem and his comeback earlier this year was stalled by a muscle tear.
Former world No. 2 Paula Badosa will skip the Games.
Nadal crashed to a defeat by fourth seed Alexander Zverev in Paris and although there were positives, he said he could not predict how his battered body would respond to the demands of the Games in July and August.
The Spaniard, who turns 38 next month, lost 6-3, 7-6 (7/5), 6-3 to Alexander Zverev.
Novak Djokovic will begin his quest for a 25th Grand Slam crown against local hope Pierre-Hugues Herbert, while top-ranked Iga Swiatek kicks off her title defence against a qualifier.
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