Manager Bobby Cox: "Chipper crushed that ball. High change-up, and he was all over it."
Jones tied Mike Piazza for 39th place all-time in home runs and opened a 3-2 lead, and 38-year-old closer Wagner gave up a one-out single in the ninth before striking out Xavier Nady and Geovany Soto to finish off the second come-from-behind win of the season.
This one was quite different than Monday, when the Braves scored six runs in the bottom of the first for a 6-3 lead en route to a 16-5 rout.
After rolling up 12 hits, two homers and eight walks in the opener, the Braves mustered five hits and two walks Wednesday. Yet it turned out to be enough.
They got four scoreless relief innings from Kris Medlen, Peter Moylan (1-0) and Wagner after the Cubs scored two unearned runs against starter Jair Jurrjens in the fifth.
"I feel like we can do a little bit of everything, win all kinds of ways," Jones said. "We can slug with you like we did the first day, and win games late like we did tonight."
Before Jones' homer, the crowd's strongest reaction had been to Troy Glaus, whom they booed after the third and fourth strikeouts of the game for the Braves' new first baseman.
Glaus also made an error in the fifth that opened the door for the two unearned runs, failing to field a bases-loaded grounder that bounced off the palm of his glove.
Braves rookie sensation Jason Heyward lashed an RBI double to give the Braves a 1-0 lead in the second inning, but that was the extent of the offensive highlights through the eighth.
Cubs starter Ryan Dempster allowed only three hits and two walks in six innings, and his nine strikeouts included six in a seven-batter span.
Jurrjens was undermined by lack of support much as he was so frequently in 2009, when he was 14-10 with the third-lowest ERA (2.60) in the National League. But this time the Braves at least rallied after he left.
"Any time the team wins, I win," said Jurrjens, who was charged with three hits, two walks and two unearned runs in five innings. "I'm happy."
Glaus, a converted third baseman, misplayed a one-out, bases-loaded grounder by Dempster to let in one run, then Ryan Theriot drove in another with a sacrifice fly to center that didn't bring a particularly strong throw from Nate McLouth.
Wednesday marked the 15th time in his past 23 starts that the Braves scored two runs or fewer while Jurrjens was in the game.
Heyward's three-run homer in his first major league at-bat Monday helped fuel a six-run first inning. He hit a two-out double on the second pitch he saw Wednesday to drive in Brian McCann in the second.
Dempster struck out Glaus and Yunel Escobar before Heyward's double.
Dempster has a 2.07 ERA in his past three starts against the Braves, with 26 strikeouts and six walks in 21 2/3 innings.
The Braves wasted a prime opportunity in the third after loading the bases on singles by Melky Cabrera and Prado and an intentional walk to McCann with first open.
That loaded the bases for Glaus, who struck out again. As did Escobar after him.
Glaus has six strikeouts in his first two games for the Braves.