Jones won the Gatorade Circle of Champions Florida Baseball Player of the Year, Regional Baseball Player of the Year, was the Runner-up National Player of the Year, and was inducted into the Florida High School Athletic Association Hall of Fame in 2012.
On March 22, 2012, the Braves announced that Jones would retire following the 2012 season, after 19 major league seasons with the team. Following the announcement, a fan tribute song called "The Chipper Jones Song" was featured in a number of sports blogs.
Jones opened the 2012 season on the disabled list, following surgery on March 26, 2012 to repair a torn meniscus in his left knee. He was activated from the disabled list and was in the lineup on April 10, as the Braves faced the Houston Astros; he went 2–4 with a single and a two-run home run, helping the Braves to their first win of the season.
Jones hit his 460th home run off Trevor Cahill of the Arizona Diamondbacks on June 27, 2012, putting Jones in 33rd position on the list of top 300 Major League Baseball home run hitters. Jones is also in 33rd position on the list of Major League Baseball career doubles leaders, passing Lou Gehrig's record for doubles during the same series with Arizona on June 29, 2012.
On July 3, 2012, Jones was named to the NL All-Star team as a replacement for the injured Matt Kemp. That same day, he had his third career five-hit game and the first since 2002. He made it known that he wished the National League would win the All-Star game in his pregame address to his NL teammates:
On August 16, 2012, Jones hit two home runs and collected his 2,700th hit. On September 12, 2012, Jones recorded his 1,500th walk in a game against the Milwaukee Brewers, becoming the first switch hitter in Major League Baseball history to obtain at least 2,500 hits, 1,500 RBIs, 1,500 runs and 1,500 walks. Jones also joined Stan Musial, Babe Ruth, Ted Williams, and Lou Gehrig as the only players in Major League history to record at least 2,500 hits, 1,500 walks, 1,500 runs, 500 doubles, 450 home runs, and 1,500 RBIs while hitting .300 with a .400 on-base percentage and .500 slugging percentage.