The Braves announced that Jones had surgery for the medial meniscus tear Saturday afternoon in Atlanta.
Recovery time is slated at two to three weeks for the 39-year-old.
"I just didn't want to play through it all summer and have something go wrong in September and have to miss the playoffs," Jones told the Atlanta Journal-Constitution on Saturday in a text message. "It's killing me to hit right-handed, so we decided to play (Friday) night, then get it done today."
Jones is batting .259 with eight home runs and 46 RBIs.
"He said we would see him Thursday," manager Fredi Gonzalez told The Associated Press. "I think the timing was perfect for him to get this (procedure) done and we get him the rest of the way, fresh legs and healthy. I know it will be a big help for us."
The Braves recalled third baseman Brandon Hicks from Triple-A Gwinnett to fill Jones' roster spot.
The Braves were in Philadelphia for a three-game set with the Phillies.
Information from The Associated Press contributed to this report.