The great rivals contested a record 60 competitive clashes during their careers, with Djokovic leading 31-29, but there will be no more after Nadal announced last week he will retire following the Davis Cup Finals in Malaga next month.
Whether he will play singles there remains to be seen, so this 6-2 7-6 (7-5) defeat may well have been a final hurrah for the 38-year-old.
There were some vintage Nadal moments, including several crowd-pleasing forehands down the line, and the Spaniard had a big smile on his face at the end.
Speaking on court to Djokovic, he said: "It has been an amazing rivalry. In a personal way I have to say that you helped me to go over my limits during almost 15 years.
"So thank you for that because without that probably I will not be the player that I am today.
"It has been a dream come true to be able to play for almost 20 years being competitive and having the chance to play in the best places in the world."
Djokovic said: "I have the utmost respect for you -- incredible athlete, incredible person.
"The rivalry has been incredible and has been very intense, so I hope that we'll have a chance to maybe sit on the beach somewhere and maybe have a little drink and reflect on life, talking about something else.
"I will finish with one big thank you, from not just me, but all of the tennis world for what you have done. You left an incredible legacy and we really appreciate it.
"Don't leave tennis man. Stay a little bit longer, stay with us."
Nadal expressed gratitude to his great rival.
"Thank you Novak for everything for all the moments we shared on court during our careers. It's been an amazing rivalry," said Nadal, whose men's record of winning 22 Grand Slam titles was broken by Djokovic.
"In a personal way, you helped me go over my limits during almost 15 years. Without that, I wouldn't be the player I am today. Congratulations for all the titles and amazing career to you and your team."
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