The 16-times Grand Slam champion, who has been slightly ill lately, was kept on his toes before racing to victory to set up a meeting with seventh seed Stefanos Tsitsipas after the Greek beat Australian Alex De Minaur 6-3 6-4.
Serbian Djokovic bagged the first set on his seventh opportunity and he did not look back after breaking for 2-1 in the second with a booming forehand winner.
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Alexander Zverev continued his post-China slump form as he lost to Denis Shapovalov, his third defeat in four matches.
The German had reached the final in Shanghai only to lose to Daniil Medvedev, but was then knocked out of the Swiss Indoors by Taylor Fritz and dropped the first set to Shapovalov in just 29 minutes.
He battled back to level the match at a set a piece but Shapovalov broke in the very first game of the decider, going on to seal a 6-2 5-7 6-2 victory.
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Rafael Nadal meanwhile racked up his 50th victory of the year as he saw off Stan Wawrinka in an entertaining but ultimately routine victory for the Spaniard.
Wawrinka needed to win the title in Paris to have any hope of qualifying for the ATP World Tour Finals but lost his serve just three games into the match and Nadal never looked back, winning 6-4 6-4 in two sets that both last 44 minutes each.
Fifth seed Dominic Thiem was knocked out in the third round when he lost 6-3 6-2 to Bulgarian Grigor Dimitrov who will play his first quarter-final at a Masters event since Canada 2018.
Dimitrov, who had been struggling since reaching the semi-finals at the U.S. Open, played brilliantly throughout, taking advantage of Thiem's fading condition after the Austrian won the title in Vienna last Sunday.
Dimitrov next takes on Chile's Cristian Garin, who beat local favourite Jeremy Chardy in three sets.
Later on Thursday, world number two Rafael Nadal, looking to lift the trophy at Bercy for the first time, takes on old foe Stan Wawrinka.
The Swiss, along with Frenchman Gael Monfils, De Minaur and Italian Matteo Berrettini, is vying for the remaining spot for the season-ending ATP Tour finals.
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