The 26-year-old will move from Evian in a reported 2.5million euro deal.
"The agreement is subject to successfully passing the medical examination, which will take place this weekend," Marseille said in a statement.
Khlifa had been a long-term target of Montpellier, but when that deal failed to materialise Marseille swooped to sign a player who has scored 25 goals in two seasons at Evian.
His 13 Ligue 1 goals last season included an audacious 65-yard strike from his own half during a 4-0 win over Nice in May.
Subject to passing his medical, Khlifa will become Marseille's fourth signing of the summer after Dimitri Payet, Benjamin Mendy and Gianelli Imbula.