The second seed needed two tie-breaks to secure victory in his second-round tie at the ATP 250 hard-court event, eventually coming out a 7-6 (7-4) 7-6 (10-8) winner in one hour 49 minutes.
In a match that only saw two breaks in serve, it was Tsonga who had enough to secure victory against the resilient Russian, still high on confidence after his win over Igor Sjisling in the first round.
Tsonga was first to break in the third game of the match but he was unable to consolidate, and allowed Davydenko to come straight back and level the set at two-games all.
Neither player offered a chance to break in the remainder of the set, with Tsonga winning the tie-break on his third set point.
After serve dominated in the second set, the Frenchman wasted one match point in the second-set tie-break, but made no mistake with his second to secure victory.
Top seed Richard Gasquet joins compatriot Tsonga in the quarter-finals after a 6-3 6-3 win over Slovenian Blaz Kavcic.
A tight opening set saw only two chances to break, both on the Kavcic serve, with Gasquet taking the first but spurning the second.
The world number nine was in complete control in the second set, breaking twice to complete the victory and set up a last-eight match with either Tobias Kamke or fifth seed Ivan Dodig.
In the final first-round matches in Marseille, eighth seed Nicolas Mahut was one of three Frenchman to seal victories.
Mahut needed 88 minutes to see off the challenge of compatriot Kenny de Schepper, winning 7-6 (7-2) 6-3.
Michael Llodra joined Mahut in the second round with a 6-3 7-6 (7-2) win over Slovakia's Lukas Lacko, while Julien Benneteau completed a good day for the home players with a 6-1 6-4 win over Jesse Huta Galung from the Netherlands.
Lithuanian qualifier Ricardas Berankis will face Mahut in the next round after his match with Czech Republic's Jan Hajek ended early due to his opponent suffering a knee injury with Berankis 6-5 ahead in the opening set.
There were also wins for Spain's Roberto Bautista Agut , who saved 12 break points to beat Dustin Brown 7-5 4-6 6-3, and Jan-Lennard Struff who came from a set behind to beat David Guez 3-6 6-1 6-1.