Aaron gave Jones a third base with the words "Chipper Jones 1993-2012." The special bases with the tribute to Jones were used in the game. The on-deck circles also carried the logo, and Jones' No. 10 was painted in the grass in center field.
Baseball commissioner Bud Selig said in a video message that Jones is a future Hall of Famer.
"It's obvious where you're headed," Selig said. "The next time we all see you will be in Cooperstown, N.Y."
Jones won the 1999 NL MVP and 2008 batting title. His 468 home runs are the third-highest total for a switch-hitter, behind Mickey Mantle (536) and Eddie Murray (504). His 1,623 RBIs are the most for a third baseman, passing George Brett and Mike Schmidt this season.
Catcher Brian McCann, representing Braves players, thanked Jones "for being our leader, our mentor." The players bought the 40-year-old Jones, who is retiring after the season, a pool table.
The Mets are a fitting opponent for Jones' final home regular-season series. Jones feasted on Mets pitching in his 19-year career, hitting .311 with 49 home runs and 159 RBIs.
Jones and the Braves have clinched at least a wild-card berth after falling out of the playoffs on the last day of the 2011 season, capping a September collapse.
Jones smiled as he looked at his teammates watching from the dugout and said "I feel like every one of you are my younger brothers.
"You have done such a great job of coming back after what happened last year," Jones said. "I'm so proud of each and every one of you."
Cox was Jones' manager for the first 17 years of his career. Fredi Gonzalez took over the Braves last season.
Cox gave Jones a final pep talk during the ceremony.
"I want to say to Chipper to keep that rope in his mouth and keep pulling Fredi and his troops to ... the World Series," Cox said.
Jones said the Braves are "one of the best organizations in pro sports."
"In 19 years I've played under two managers and two general managers," Jones said. "Not too many organizations can boast of that over a two-decade period. That just shows you how solid this organization is from top to bottom."
The team also gave Jones and his family a trip to Hawaii and a plaque made from Turner Field bricks and shaped like home plate. Team president John Schuerholz announced Jones' clubhouse locker will be moved to Jones' home.
Jones was given a proclamation in which Georgia Gov. Nathan Deal proclaimed Sept. 28, 2012 as "Chipper Jones Day" in the state.
Jones' parents and two of his sons joined him on stage.
New York's Ruben Tejada hit the game's first pitch to Jones, who had a wide grin after making the pickup -- with a slight bobble -- and then throwing out the shortstop.