The 33-year-old Nadal, who can secure the end-of-year top ranking ahead of Djokovic by winning his maiden Bercy title, beat French wildcard Jo-Wilfried Tsonga 7-6 (7/4), 6-1.
France's Gael Monfils failed to snatch the remaining spot for the season-ending ATP Finals after he was crushed 6-2 6-2 by Canadian Denis Shapovalov.
The 16-time Grand Slam title-winner is chasing a record-extending fifth Bercy crown and will next face world number seven Stefanos Tsitsipas, who beat Alex de Minaur 6-3, 6-4.
Tsitsipas, encouraged by a packed crowd, avoided a first-set bagel by saving three set points, only for Djokovic to serve it out in the following game after a mere 28 minutes on court.
But Nadal stepped it up in the tie-break, with two incredible winners on the run helping him take a crucial one-set lead.
The 19-time Grand Slam champion saw off Wawrinka´s challenge with a break to lead 5-4 in the second set and served out the match to make it his seventh Paris Masters quarter-final in as many appearances.
Shapovalov's victory over Monfils, who had previously beaten him in the U.S. Open just a couple months ago, marks the fourth time that he has reached a Masters 1000 semifinal in his career, and he finished the season as the No. 1 ranked Canadian and ATP top-20 player for the first time in his career.
Should he fail, Italian Matteo Berrettini, who was eliminated in the second round here, will earn the spot for the November 10-17 event at the O2 in London. "I lost to Stefanos in Shanghai and obviously I went through the videos, understanding what I did well, what I didn't do so well", Djokovic said.
Djokovic holds an 8-1 winning head-to-head record against Dimitrov.
Djokovic said he played "one of his best matches of the season" to thrash Tsitsipas.
Victory enabled the Spaniard to reach the semi-finals in Paris for the first time since 2013.
"He (Tsitsipas) is one of the best players in the world", said Djokovic. "I am playing knowing that it's a hard tournament, you need to be focused to hold your serve and take advantage of the few chances you have on return".
Greek youngster Tsitsipas was a 6-3 6-4 victor against Australian Alex de Minaur, while Rafael Nadal dug deep for a gritty 6-4 6-4 win over Stan Wawrinka. "I don't play too bad myself, so it's going to be for sure a good one".
Dimitrov, who had been struggling since reaching the US Open semi-finals, played brilliantly throughout, taking advantage of Thiem's fading condition after the Austrian won the title in Vienna last Sunday.