Tsonga started his 2009 season in Australia at the Brisbane International tournament. He defeated Agustín Calleri, Jarkko Nieminen, and then lost Richard Gasquet in the quarterfinals. Tsonga teamed up with fellow Frenchman Marc Gicquel to win the doubles title by defeating Fernando Verdasco and Mischa Zverev in the final. At the Medibank International, Tsonga was forced to retire with a back injury before his quarterfinal match against Jarkko Nieminen.
The Australian Open found Tsonga making it to the quarterfinals, before losing to Spaniard Fernando Verdasco in four sets. His rank went down to No. 14. He next entered the South African Tennis Open in Johannesburg, where he won his first title of the year, and third overall, by defeating Jérémy Chardy in the finals. After his triumph in South Africa, Tsonga entered the ABN AMRO World Tennis Tournament in Rotterdam, where he lost to World No. 1 Rafael Nadal in the quarterfinals in three sets.
Tsonga then entered the Open 13 in Marseille. He defeated Andrey Golubev, Simone Bolelli, and Feliciano López, before notching his fourth straight win over Novak Djokovic in the semifinals. In his second all-French final of the month, he defeated Michaël Llodra to win his second tournament in three weeks.
Tsonga was then called up to play the singles matches for France against the Czech Republic in their Davis Cup first-round clash. Tsonga defeated Radek Štěpánek, but the Czech Republic had an insurmountable 3–1 lead. Tsonga gave France a consolation point by beating Jan Hernych.
At the BNP Paribas Open in Indian Wells, California Tsonga made an early exit from the tournament, as he was defeated by the Russian Igor Andreev in the third round. Next up for Tsonga was the Sony Ericsson Open in Miami. He defeated Agustín Calleri, Robert Kendrick, and Gilles Simon, only to lose to Novak Djokovic in the quarterfinals. After skipping two tournaments, Tsonga made his return at the Internazionali BNL d'Italia in Rome, but he lost his first singles match in the clay-court season at the hands of Richard Gasquet. In doubles, he and partner Julien Benneteau lost to the Polish pair of Mariusz Fyrstenberg and Marcin Matkowski in the second round.
Tsonga then entered the Madrid Masters, but lost in round two. Afterwards, he received the 2008 ATP Most Improved Player of the Year award.
Tsonga then represented France at Düsseldorf, Germany in the ARAG World Team Cup. Tsonga won the first tie against Sweden's Andreas Vinciguerra, but lost in doubles. Tsonga was defeated by German Philipp Kohlschreiber, but then beat American Robby Ginepri. However, France lost three successive ties during the week
Tsonga then entered the French Open. Tsonga recorded his first-ever match win at Roland Garros by defeating Julien Benneteau in the first round. He then had wins over Juan Mónaco and Christophe Rochus, before his fine run ended at the hands of fifth seed Juan Martín del Potro. Next up was the Gerry Weber Open, Tsonga suffered a straight-set defeat against German Tommy Haas in the second round. However, In doubles, Tsonga was paired with his French compatriot Marc Gicquel, but they were also defeated in round two.
Tsonga then entered Wimbledon. He survived a tough four-set against Andrey Golubev and received a walkover from Simone Bolelli, before losing to Ivo Karlović of Croatia. At the Legg Mason Tennis Classic in Washington, D.C, Tsonga lost to the American John Isner in the second round. Tsonga made his debut at the Rogers Cup in Montreal, Canada. He defeated Rainer Schüttler and Gilles Simon. In the quarterfinals, he overcame World No. 1 Roger Federer, coming back from an injury timeout after winning the first set by a dive-volley, as well as being 1–5 down in the third set. He advanced to the semifinals, where he lost to Andy Murray in straight sets.
At the Western & Southern Financial Group Masters in Cincinnati, Tsonga made an early exit from the singles category, unexpectedly losing to World No. 124 Chris Guccione of Australia. In doubles, Tsonga and Michaël Llodra lost to Mahesh Bhupathi and Mark Knowles in the quarterfinals.
The US Open started well with victories over Chase Buchanan, Jarkko Nieminen, and Julien Benneteau. However, Tsonga lost to 11th seed Chilean Fernando González in the fourth round. Tsonga then represented France at the Davis Cup playoff round against the Netherlands. Tsonga defeated the Jesse Huta Galung Thiemo de Bakker in singles and, with partner Michaël Llodra, won in doubles over Thiemo de Bakker and Igor Sijsling, wrapping up the tie 4–1.
Tsonga then entered the PTT Thailand Open, where he was the defending champion and top seed, as Rafael Nadal withdrew just days before the tournament began. After two close matches, Tsonga crashed out to the young Serbian Viktor Troicki in the semifinals. Tsonga also competed in the doubles category with Fabrice Santoro, but they lost to Mischa Zverev and Guillermo García-López in the semifinals. At the Japan Open in Tokyo, Tsonga defeated Mischa Zverev, Richard Gasquet, Ernests Gulbis, and Gaël Monfils to reach the final. There, he beat Mikhail Youzhny in just over an hour to clinch his third title of the season and his first-ever ATP World Tour 500 title. In the doubles category, Tsonga paired with Swiss Stanislas Wawrinka, but they were defeated in the second round.
Next up was a trip to China and the Shanghai Masters. Tsonga defeated Zeng Shao-Xuan, but lost to Robin Söderling in the third round. In doubles, paired with Julien Benneteau, Tsonga made it to the finals, where they beat sixth seeded Mariusz Fyrstenberg and Marcin Matkowski to win their first-ever ATP Masters 1000 doubles title. After two disappointing tournaments at Lyon and the Valencia Open, Tsonga entered the Paris Masters, where he was the defending champion. He had wins over Albert Montañés and Gilles Simon, but lost to World No. 2 Rafael Nadal in the quarterfinals.
Tsonga ended his 2009 season staying in the top 10 for the second year in a row.