Tsonga, eliminated after losing his first two Gold Group matches in his debut at the season-ending tournament, looked listless early before coming alive and winning five consecutive games from 5-5 in the second set to take control.
The Frenchman acknowledged that he was fortunate to win.
"He was better than me in the two first sets, but I take the second one,'' Tsonga said. "It was a holdup.''
Djokovic beat Tsonga in the Australian Open final in January for his first Grand Slam title but now has lost their past three meetings, including at the Paris Masters two weeks ago.
Tsonga, who has won over fans in Shanghai with passionate play and powerful serves, was unusually subdued early in the match, showing only flashes of the form that carried him to the title in Paris - an event he had to win to qualify for this tournament.
Djokovic, continuing his efforts to end the stranglehold that Federer and Rafael Nadal have had on the top two spots in the rankings, broke Tsonga twice while finishing the first set in just 25 minutes.
Tsonga pulled himself together in the second set, saving two breakpoints while serving at 2-2, then finally broke through as Djokovic served at 5-6. The Serb had four unforced errors in the game, sending a forehand long on set point.
Another four mistakes handed Tsonga an early break in the third set. Tsonga broke again, at love, to take a 5-1 lead, then held at love, flicking a lob winner on match point.
"In the third set especially, he played well,'' Djokovic said. "I made some unforced errors. The important thing is that I'm through.''
Four-time Masters Cup winner Roger Federer also has to win Friday to get through. He faces Britain's Andy Murray, who is 2-0 in the Red Group and already has guaranteed himself a place in the semis.
Gilles Simon of France still has a chance if Federer falters. He will play 26th-ranked Radek Stepanek, who replaced Andy Roddick when the American pulled out Wednesday with a sprained ankle suffered in practice.
Simon got into the elite field when top-ranked Nadal withdrew before the tournament began with a sore knee. The Frenchman then downed Federer in his first match.
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