But Jones shocked everybody, including himself on Tuesday, when he arrived at Turner Field and proved that his right leg was healthy enough for him to resume playing. Just two days earlier in Toronto, he'd said that there was a "distinct" possibility that his strained right quadriceps muscle would force him to the disabled list.
"Sunday was probably one of the worst days for me," said Jones, who leads the Majors with a .394 batting average. "I really had no hope of playing. Maybe it was just one of those bad days for me."
If Sunday was a bad day for Jones, then Tuesday was a great day for Cox, who gladly put both Jones and Mark Kotsay back in the starting lineup for the series opener against the National League East-leading Phillies. Kotsay had been out since May 26 with a lower back strain.
Jones, who leads the Majors with a .393 batting average, responded by recording a recording a double and drawing two walks in his five plate appearances. He showed no hesitation when he lofted a ball into right-center and then hustled to turn a single into a double to begin the bottom of the sixth inning.
Things should continue to improve for Cox on Wednesday, when he hopes to put shortstop Yunel Escobar back in the starting lineup. Escobar hasn't played since straining his left shoulder while sliding back into first base on June 24.
"I thought we might have to disable two [players] tonight," Cox said. "Now we might not have to disable anybody."
Cox thought there was a chance that he might need to put both Jones and Omar Infante on the 15-day disabled list. But Infante's right hamstring has steadily improved since he strained it on Wednesday, and he was available to come off the bench on Tuesday.
While Infante's availability was important, Jones' return to the lineup for the first time since June 20 was a pleasant surprise that couldn't have come at a better time. The Braves enter this series trailing the front-running Phillies by four games and they are just 4-12 in games that Jones has not been in the starting lineup.
"Until I got here today, I didn't really know if I'd be able to play," said Jones, who had made three pinch-hit appearances since aggravating his quad muscle during a June 20 game against the Mariners.
Jones said the importance of this series against the Phillies played a part in his decision to return on Tuesday. But essentially, he was able to avoid the disabled list because he finally gained the ability to stretch and run without any discomfort.
"My quad is not 100 percent," Jones said. "But I said when I could beat out a double play, score from first [base] on a double and things you need to do as a baseball player, that I would get back in there. I can do that now."
When Jones awoke on Monday, he was surprised to find that he could finally stretch his quad muscle without the pain that had been present just one day earlier. But he wasn't truly confident that he'd be ready to play until late Tuesday afternoon, when he ran sprints between first and second base.
When he was done running, Jones told Cox that his right leg had made great improvement. Then, about an hour later, he told his longtime manager that he was ready to return to the starting lineup.
"I expected to have some pain [when I ran]," Jones said. "Granted, I didn't go 100 percent. But I did push it up to 75 or 80 percent and I was relatively pain-free."
Mark Bowman is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.