"It's definitely frustrating, realizing how good a team we have and how we've fallen short," Barrett said of the Cubs, who started the day 6 1/2 games back in the Wild Card race. "Whenever you fall short of expectations, it's really tough."
With the game tied at 2 and one out in the Braves' ninth against Kerry Wood (3-4), Marcus Giles singled and Jones followed with his second homer of the game off a 2-2 slider.
The Cubs wasted a solid performance by Carlos Zambrano, who struck out 10 and gave up three hits over eight innings but didn't get a decision.
"It's a three-hit sequence there [for Zambrano], and I give up two hits and two runs," Wood said. "Good timing for them, bad timing for us."
"[Zambrano] pitched great. He certainly pitched well enough to win," Cubs manager Dusty Baker said. "It was just a matter of too much Chipper Jones. They said Chipper was hot, and he certainly was hot. He hadn't hit Woody well in his career. He got Woody tonight. Chipper, he's hot."
It's the first decision for Wood since July 20, which was his last start. This was his ninth relief appearance since then. Lifetime, Jones was 4-for-21 against Wood.
"I've lost games before," Wood said. "I'll be fine."
Tim Hudson (10-7) gave up two runs on seven hits in his 17th career complete game and first this year. The Cubs haven't been able to take advantage of Wrigley Field and now are 30-31 at home.
Zambrano deserved better. The right-hander retired the first nine batters he faced before Rafael Furcal doubled to lead off the Braves' fourth. Furcal advanced on a sacrifice, and Jones followed with his 12th home run to take a 2-0 lead.
"I missed a spot," Zambrano said of his home run delivery to Jones. "I tried to throw a fastball outside and the ball came out of my hand where I don't want to throw the ball. That was a big mistake. If I walked Chipper in that situation, and I get a ground ball with the next hitter, I win the game, 2-0. Baseball is like that."
Instead, Andruw Jones singled after Chipper's blast, and Zambrano then retired 14 in a row.
"Zambrano was throwing great," Atlanta manager Bobby Cox said. "It was a matter of who was going to get a break. Chipper got a pitch right there and hit it."
The Cubs missed an opportunity in the fourth. They loaded the bases and scored a run when Aramis Ramirez grounded into a double play.
"That's a sign of a good pitcher, making pitches when he had to," Lee said of Hudson. "Not many times are you going to get Aramis in that situation. That's what [Hudson] does -- sinkerball pitcher gets ground balls."
But that was it until Lee tied the game with a leadoff homer in the Chicago seventh, only the third hit off Hudson. With the blast, Lee tied Ernie Banks for the club record for most home runs in a season by a first baseman. Banks hit 37 in 1962.
"Ernie Banks was a great player, so it's nice to be mentioned with him," Lee said.
Barrett tried to score from second on Neifi Perez's single with two outs in the inning, but he was thrown out at the plate by left fielder Kelly Johnson.
"In that situation, you've got to take a chance, especially because Corey [Patterson's] not going real good right now," Baker said. "You've got to take a shot right there. He threw it on target."
Barrett felt he had a good chance.
"I thought that if I ran as hard as I could, that I could score easily," he said. "I saw Corey behind home plate telling me to slide and I just ran for my life. I couldn't believe it was a close play. [Catcher Johnny Estrada] had the ball before I started my slide. It was a great play on their part."
The Cubs still have six weeks to go.
"We can't think about frustration," Zambrano said. "We just have to keep on going. We have 1 1/2 months to go. The last month will decide it for us. Let's keep fighting."