Jones, who won the Philip Morris title earlier this month, will be trying to make it two in a row.
Hidemichi Tanaka of Japan carded 5-under 67 for second place with compatriot Takashi Kanemoto alone in third with a 4-under 68.
Australian Aaron Baddeley was in a group of four golfers who shot 3-under 69s. They're four off the pace.
Two of the big, young guns in the field, American Charles Howell III and England's Justin Rose, both opened with 2-under 70s and are in a tie for eighth.
Rose will be attempting to make it two wins in just two appearances on the Japanese tour this year, as he won the Chunichi Crowns tournament in May.