The lone hit by Casey Kotchman was a sixth-inning solo homer.
Martin Prado had two hits and one RBI.
Single runs scored on errors by Jake Fox in the third and Kosuke Fukudome in the ninth, while Nate McLouth had two runs and two hits for the Braves, who won twice in the three-game series.
They played a second straight day without star third baseman third baseman Chipper Jones (right groin).
Chicago's run scored on Fukudome's sixth-inning homer.
Ryan Theriot had two of the six hits for the Cubs, who have lost three of five.
The losing pitcher was Kevin Hart (0-1) in his first major league start.
Cubs catcher Geovany Soto (mild left oblique strain) is day-to-day.