The Spanish world No2 was made to work for the win, dropping the opening set in an eventual 4-6, 7-6, 6-4 victory.
In doing so, he joined an elite group of players with 1,000-plus wins on Tour: Jimmy Connors, Roger Federer and Ivan Lendl.
“One negative thing about 1,000 wins is you are very old because to win 1,000 matches you need to have a very long career but I am super happy,” Nadal said afterwards.
“To arrive at that number I must have done a lot of things well.
“I’m proud of a lot of things but I faced some challenges in my career in terms of injuries.
“It’s a big achievement to be playing at the age of 34.”
And he remains on course for the end-of-season ATP Finals in London later this month.
Nadal next faces Australian Jordan Thompson in the last 16 in the French capital.