But many baseball fans will remember that their relationship actually dates back to 1990, when Cox, then the Braves general manager, chose to select Jones with the first overall selection in the First-Year Player Draft.
As Jones announced on Thursday morning that he will retire at the conclusion of this season, Cox reminisced about the first time he accompanied legendary Braves scout Paul Snyder to watch a young kid named Chipper Jones from Bolles High School in Jacksonville, Fla.
"I would always tell Paul Snyder, don't let me know which player we're looking at when they were exercising," Cox said. "I wanted to be able to pick them out. I went on some road trips with Paul and I could never pick out the guy.
"Well we go up to Bolles High School and I tell Paul the same thing, 'Don't tell me which one is Chipper Jones.' They didn't have numbers on their jerseys. They were working out in their T-shirts. I said, 'Paul, I think it's the third guy in the first row from the right.' He said, 'You finally got one right.'
"That was Chipper Jones. He stood out like a sore thumb. He was a great athlete. I've been the lucky one for all of these years to have players like Chipper Jones. It made my career. I never would have lasted as long as I did if we didn't have guys like Chipper Jones."
Long before winning his 1999 National League Most Valuable Player Award or establishing himself as one of the greatest switch-hitters, Jones remembers looking into the stands during high school practice and seeing both Snyder and Cox in attendance. He just happened to hit 20 home runs with 25 batting-practice swings, barehand a bad-hop grounder and show off his plus arm on that particular day.
"I remember having the absolute most perfect day at the ballpark that I've ever had in my life while they were sitting in the stands," Jones said. "I was thinking after that day, if they think there is another guy on the planet that is better to take number one, then I want to see this guy. I really thought I won them over that day."
Five years later, Jones would begin his reign as Atlanta's starting third baseman, a role he will maintain through the end of this season.
"He is still a very productive Major League player," Braves manager Fredi Gonzalez said. "If he can give us the same numbers that he did last year, we'll be all for it. I told him I didn't want to say goodbye or congratulations until late in October some time."
Jones' Hall of Fame credentials include a .304 batting average, 454 home runs and 1,561 RBIs. He and his boyhood idol Eddie Murray stand as the only switch hitters who have compiled 2,500 hits and 1,500 RBIs in his career.
"Not everybody can say they played with a first-ballot Hall of Famer," Braves pitcher Tim Hudson said. "It's an honor for me to be able to say I played with him for eight years. It's not going to make him feel real good, but I grew up watching him play."
The 36-year-old Hudson was actually in college by the time Jones became an everyday part of the Braves' lineup. Jason Heyward was actually just 4 years old when the veteran third baseman made his Major League debut on Sept. 11, 1993.
"It's been a privilege to play with him," Heyward said. "He's a good teammate and a good friend. He's a significant part of the glue that holds this team together."
While Jones plans to spend some time with his family before potentially beginning a career as a hitting coach, he admits he has enjoyed the opportunity to mentor his teammates in the art of hitting. Six-time All-Star Brian McCann praises the veteran third baseman's knowledge, and Matt Diaz is among those teammates who believe Jones prolonged their Major League career.
With his batting average sitting at .243 on May 9, 2006, Diaz received some advice from Jones. He tripled that night and then went 5-for-5 in a win against the Marlins two days later. Suddenly, he was no longer fearing a return to the Minors.
"Professionally and financially, I can't thank him enough for what he did for me and my family," Diaz said. "I tell him all the time, 'It's a shame you made so much money because you would have been a heck of a hitting coach.' I tell him if I ever become a manager, I'm going to find him some exclusive deer hunting land for payment to come be my hitting coach. He'd be one of the best, if not the best hitting coach ever.
"I don't know if it's because he had to work from both sides of the plate. A lot of times you run into guys who were just natural talents and they can't teach hitting. He's not that way at all. He knows exactly what he's doing with his swing."
Before joining the Braves last year, Dan Uggla heard about Jones' expertise in the art of the swing. Over the course of the past two seasons, he has gained an even greater appreciation.
"One thing I always heard was if you get in his head about hitting, you might get lost in there," Uggla said. "He is one of those guys who knows so much about hitting. It's just tough to keep up with. He's a very intelligent man and extremely athletically talented.
"It was a dream come true to be able to play with a player with that kind of talent, professionalism and knowledge of the game."
Mark Bowman is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.