The team called it a sprain, but Jones said after the game that he wasn't sure what was wrong.
"It's hurt," he said. "I heard a distinct pop. I don't think it's my ACL because when I did it before it sounded like my knee exploded. It sounded like the whole stadium could hear it pop. While I did hear it pop, it wasn't the same pop."
Jones grabbed a grounder hit by Hunter Pence and jumped in the air as he made the throw to first base to get Pence out.
He then fell to the ground where he remained for several minutes while trainers and coaches crowded around him. He was helped to his feet and walked gingerly off under his own power. He was replaced by Brooks Conrad.
The 38-year-old Jones, who is hitting .265 this season, had a double on Tuesday.
He will have an MRI on Thursday in Atlanta.
Jones had the knee covered in a bandage after the game but said it wasn't very swollen, which he believes is a good sign. Still, he's worried about what he'll find out when he returns to Atlanta.
"I've got a very distinct pain on the lower left side of my knee," he said. "I don't know what that means. Hopefully it's just a sprain. [We] just got to wait for the MRI."