ATLANTA — Jeff Francoeur hit a tying two-run homer with two outs in the ninth and Chipper Jones drove in the winning run with a 12th-inning single, helping the Atlanta Braves rally for a 6-5 victory over the Chicago Cubs on Tuesday night.

The Cubs wasted a brilliant performance by rookie starter Randy Wells. Filling in for suspended Carlos Zambrano, he didn’t allow a hit until Jones singled with two outs in the seventh.

Alfonso Soriano and Derek Lee homered for Chicago, which couldn’t hold a 5-0 lead.

Garret Anderson started the comeback with his second homer in as many games — a leadoff shot off Wells in the eighth — and the Braves scored two more runs in the inning without a hit, taking advantage of two walks, a hit batter and an error.

The Cubs were still one out from the win when the struggling Francoeur, a former phenom now being mentioned in reports of a possible trade, tied it with a drive into the left-field seats off Kevin Gregg.

The Braves got runners to third in the 10th and 11th but couldn’t score. Finally, Jones ended it with an opposite-field single to left off Aaron Heilman (2-3) that brought home Yunel Escobar, who had singled and stole second.

Rafael Soriano (1-0) earned the win with two scoreless innings.

After doing nothing offensively most of the night, the Braves suddenly came alive — with help from the Cubs. After Anderson’s homer, first baseman Lee dropped a routine throw to first that allowed Martin Prado to reach.

The Cubs went to their bullpen, but Carlos Marmol walked Francoeur, hit Greg Norton and walked Kelly Johnson to force in a run. Escobar followed with a sacrifice fly to make it 5-3.

Chicago went to Gregg in the ninth. He got two outs, sandwiched around a strikeout that put a runner aboard. Anderson whiffed at strike three in the dirt, but took off for first when the ball got by catcher Geovany Soto and rolled all the way to the backstop for a wild pitch.

That came back to haunt the Cubs when Francoeur drove a 2-1 pitch into the seats in right-center for just his fourth homer of the season. He got a helmet-pounding reception from his teammates when he arrived back at the dugout. Soriano put Wells ahead before he even went to the mound, leading off with a homer for the 54th time in his career. Soriano broke a tie with Craig Biggio in that category and now trails only Hall of Famer Rickey Henderson, who had 81 leadoff homers. Wells, in just his eighth big league appearance, faced the minimum until Jones’ single. Atlanta’s only baserunner up to that point was Escobar, dubiously awarded first after falling backward on a high, inside pitch in the fourth, as though he had been hit. The replay appeared to show the ball only striking Escobar’s bat.

Wells, who had started four games since being recalled from the minors in early May, wasn’t even supposed to start the opener of a three-game series in Atlanta. It was Zambrano’s spot, but he’s serving a six-game suspension for a tirade against the umpires in his last start against Pittsburgh.

Not that Wells was a bad option. He had a 1.80 ERA through the first four starts of his career, but a lack of support — the Cubs managed only six runs in those games — left him without his first big league win. This time, it was a late-inning collapse.

Notes: Cubs RHP Rich Harden threw a side session before the game and is scheduled to throw another Thursday. ... RHP Ryan Dempster, who left his last start with the Cubs because of a blister, threw on the side and should be ready to go Friday at Cincinnati. ... Anderson has a 10-game hitting streak. ... Chicago OF Milton Bradley left in the fourth after straining his right calf running out a grounder. He is day to day.