Jones said he was talking to a reporter when his back started bothering him.
"It's crazy," Jones said. "Seriously, it was feeling like somebody sledgehammered me in the back."
Jones said after the game the spasms were gone but he was still experiencing some pain when he turned to either side. Martin Prado replaced him at third base against New York, and Jones was unsure when he would be back in the lineup.
"I hope I'll go home, have a great night of sleep and wake up and feel great in the morning," Jones said. "Judging the way I feel now I would say that's doubtful but we got an off day on Monday so I'm hoping worst-case scenario is when we get to Washington on Tuesday."
Jones hadn't missed a game this season before Saturday and was off to a fast start. The Braves slugger was 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. He went 0-for-4 with three strikeouts in 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.