World number eight Tsonga, who saved five match points in his quarter-final against Australian Bernard Tomic, was trailing 5-6 in the second-set tie-break but hit back-to-back aces to push the Czech to a decisive set.
The Frenchman eventually put an end to his losing run against the top-seeded Berdych, having lost their three previous encounters including the latest in the ATP World Tour finals round-robin in November.
The local favourite had two break points in the third set's third game and broke serve to clinch his second title in Marseille after his 2009 triumph.
Tsonga said after the game he was proud of his resilience having struggled in the two first sets.
"I only focused on survival," he told a news conference.
"Nothing was going my way. He played far better than me in the first part of the match. He was serving well and my position on the court was bad. But I deserve credit because I never gave up. A lot of players would have done so."
Tsonga, who lost an epic Australian Open quarter-final to world number two Roger Federer in January in his first event under new coach Roger Rasheed, said this successful week has shown he was on the right path.
"I have been working hard for some time, I make sacrifices. I do everything I can to be on top and I still improve."