Jones had trouble straightening up and was heard telling a clubhouse attendant, "I just threw my back out," although the Braves later described the injury as back spasms.
It was not known yet whether Jones, who recently missed a game because of back pain, will have to go on the disabled list.
Jones is off to a fast start this season, hitting a major league best .433 with seven homers and 20 RBIs in 23 games. He also has a .310 average with 19 homers and 53 RBIs in 84 career games at Shea Stadium.
Atlanta also was without shortstop Yunel Escobar, who shattered the fingernail of his right index finger when he was hit by a sinker in the Braves' 6-3 win Friday night. X-rays were negative but he probably will be sidelined until at least Tuesday.
With Escobar out, the Braves purchased the contract of Brent Lillibridge from Triple-A Richmond and started him at shortstop against the Mets. It was his major league debut.
Right-hander Phil Stockman was optioned to Atlanta's top farm club and right-hander Zach Schreiber was designated for assignment to make room for Lillibridge.