The top-ranked Serb broke Muller’s serve once in each set and sealed victory with an ace.
Celebrating his win, Djokovic tapped his hand against his heart and made a throwing gesture to all four sides of the court as if to share the moment with the crowd.
Djokovic has a special bond with Paris, having won this tournament four times overall and having also clinched the French Open in June to complete his haul of all four majors.
“It’s a moment of happiness. It’s a real pleasure to come back to Paris after what I did at Roland Garros this year,” Djokovic said. “In the last few years I’ve played my best tennis here. It’s the end of the season and you have to find that last bit of energy.”
The second set was going with serve, and Djokovic was forced to save the only break point he faced.
But when Muller conceded his only chance on serve in the second set, Djokovic pounced. With the score 4-4 and 30-40, Muller sent down a strong serve that Djokovic returned powerfully. It seemed to surprise Muller, who whipped a forehand into the net to concede the game.
Muller sent a forehand wide to give Djokovic two match points, and the Serb sent his ace straight down the middle before milking the applause.
He improved to 4-0 in career meetings against the 33-year-old Muller.
“It’s not easy to break Gilles, but I played well,” said Djokovic, who conducted his court-side interview in French.
The 12-time Grand Slam champion faces Grigor Dimitrov in the third round and has a 5-1 career record against the 14th-seeded Bulgarian.
Later Wednesday, second-ranked Andy Murray faced Fernando Verdasco and U.S. Open champion Stan Wawrinka took on Jan-Lennard Struff.
Murray, runner-up last year, can take Djokovic’s No. 1 ranking if he wins the tournament and Djokovic fails to reach the final.
Earlier, Kei Nishikori posted his 300th win to also reach the third round.
“This year has been pretty good,” Nishikori said.
The fifth-seeded Nishikori, who made it to the semifinals here two years ago, will next face 11th-seeded Jo-Wilfred Tsonga, who beat Spaniard Albert Ramos-Vinolas 6-3, 6-4.
Nishikori has recovered well from the hip injury that forced him to retire in Tokyo last month. He reached the final in Basel last week and will be playing at the ATP finals later this month in London for the third time.
David Goffin kept alive his slim chances of joining Nishikori in London by defeating Nicolas Mahut 7-6 (5), 6-3, but the Belgian must win the title in Paris to clinch one of the two remaining spots.
Among those who can still qualify is ninth-seeded Marin Cilic, who set up a third-round match with Goffin by winning 7-6 (7), 6-2 against Ivo Karlovic.
“I’m really excited and satisfied with my form,” said Cilic, who won the Swiss Indoors last week.
In other second-round matches, 13th-seeded Lucas Pouille of France rallied past Feliciano Lopez 6-7 (1), 6-3, 6-4; American Jack Sock beat sixth-seeded Dominic Thiem 6-2, 6-4.; and Frenchman Gilles Simon rallied to beat Spaniard Roberto Bautista Agut 2-6, 6-1, 7-6 (6).
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