However he was able to recover, and claimed the title in a 7-2 fourth set tie-break.
"I'm so proud to be the first Serb to win a grand slam," Djokovic said after the match.
"I'd like to thank all the Serbian fans for coming out to support me.
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"Jo-Wilfried played an unbelievable tournament, he should be proud of himself."
Novak Djokovic |
"Jo-Wilfried played an unbelievable tournament, he should be proud of himself.
"If he won tonight it would have been absolutely deserved, well done for your success," the Serb told his opponent.
Djokovic, nick-named 'The Joker' for his light-hearted approach to the game, endeared himself to the Melbourne Park crowd by adding: "And I know the crowd wanted him to win more. But it's alright, I still love you guys, don't worry."
The Serb had been labouring after chasing down a Tsonga drop-shot in the fifth game of the set and was forced to call for the trainer.
The 20-year-old, however, did not seem to be hampered by the injury when he returned and neither man was able to break serve in the fourth set.
Tsonga moves up the rankings
Djokovic, who lost last year's US Open final to Roger Federer, raised his game in the tiebreak, taking two points on Tsonga's serve and sealed it when the Frenchman's forehand sailed wide.
"Thanks to Novak for a good fight, and is was a good moment for me to play you tonight," Tsonga said afterwards.
Tsonga, bidding to become just the second Frenchman to win a grand slam singles title in the Open era, had taken a surprise one-set lead when he recovered from losing the first game of the match to break Djokovic in the second and 10th games.
Both players held serve in the second set until Djokovic broke in the seventh game and he went on to level the match at one set apiece.
Djokovic then stepped up a gear in the third when he broke the 22-year-old in the third game.
The pair traded service games with neither really threatening to break until the final game of the third set, before the Serb made no mistake on his seventh set-point opportunity to take the set 6-3.
Djokovic will remain at number three in rankings behind Roger Federer and Rafael Nadal after his win, but Tsonga is projected to climb to 18 from 38.