Jones, who has been nagged by the injury for two months, reinjured the right quad while attempting to score from second base in the fourth inning. He also grimaced while swinging and missing on an offspeed pitch in the sixth.
Jones said that he had an egg-sized knot in his right quad that severely limited his mobility. He said he had no choice but to take himself out after the seventh inning.
The Braves third baseman was held out against the Phillies on June 8 because of the small tear in his right quadriceps and was relegated to pinch-hitting duties two days later against Chicago.
"I missed a couple of days last time and it's worse now," said Jones, whose average dipped to .390. "It's at least a couple of days."
Jones said that the pain he is now experiencing is "definitely the worst."
Shortstop Yunel Escobar sustained a strained right hip flexor while avoiding a tag at home in the eighth inning. He is listed as day-to-day and did not know how many games he would be miss. He did not walk with a noticeable limp in the clubhouse after the game.
Escobar was replaced at shortstop by Omar Infante, who had started in left and who made an error at short in the ninth inning. Ruben Gotay, who had started at second, played third base in Jones' absence.
Ryan Lavner is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.