The 39-year-old Djokovic dropped the first set but recovered to beat the French left-hander 4-6, 6-3, 6-4 on his first appearance in Basel since 2011.
"It was a super tight match, very intense from the beginning," he said.
"I was under attack from the very first point. I had to weather the storm, but I managed to find my rhythm at the beginning of the second set.
"After that, I started feeling a bit more comfortable with his tempo. Overall, it was a huge challenge. I succeeded in managing to find the solutions in a tough match today."
Djokovic strengthened his chances of a record 19th qualification for the ATP Finals by winning the China Open in Beijing earlier this month, the 102nd title of his career.
That was followed by an early exit at the Shanghai Masters, with the 24-time Grand Slam champion accepting a wildcard into the Swiss event after slipping to 11th in the Race to Turin standings.
Djokovic is a seven-time winner of the ATP Finals, but he did not compete at either of the past two editions because of injury. Only the top eight players qualify for the November 15-22 showpiece, although Jannik Sinner has already pulled out due to a knee problem.
Fourth seed Djokovic takes on Germany's Jan-Lennard Struff in the next round in Basel. He holds an 8-0 record against Struff.
