The crowd of 45,190 rose to its feet after Jones' name was announced. St. Louis catcher Yadier Molina called time and walked slowly to the mound to give Jones time to enjoy the moment.
Jones, 40, announced in Spring Training that this would be his last season. The veteran was surprised by the 45-second ovation. He stepped out of the batter's box and tipped his helmet as the crowd noise grew even louder.
"That was very classy by the St. Louis fans," Jones said. "They are widely regarded as the best fans in baseball and they showed it. I'm not used to getting that kind of reaction on the road."
At first, Jones was stunned by the tribute.
"I didn't know what to do," he said. "Kudos to Yadi for giving me that moment."
The ovation came at a key spot early in the game. The Braves had scored and were on their way to a 2-0 lead when the fans took time away from their loyalty to honor Jones.
"It was nice," said closer Craig Kimbrel. "We've gone through a few ballparks this season and they've honored him before the game. But for that to happen during the game, it was a really cool thing to see."
Jones, who went 2-for-4 in the 12-inning affair, said he has always loved playing in St. Louis because the fans have a high level of respect for the game.
"This was not expected, but it was much, much appreciated," Jones said.
The gesture came on a night when the St. Louis organization retired the uniform of former manager Tony La Russa in a pregame ceremony. La Russa's No. 10 was mowed into the center-field grass as part of the honor.
Jones also wears No. 10, which led to some good-natured ribbing from his teammates.
"The guys were making fun of me saying that St. Louis is such a classy organization that they mowed No. 10 into the grass for me," Jones said with a laugh.