Colon (1-4) pitched out of a bases-loaded jam in the seventh that preceded a rain delay of 1 hour, 59 minutes.
"That was awesome," Colon said. "You have to keep the game as close as you can."
Maddux (7-6), making his 622nd start and first appearance in Atlanta since leaving the Braves to sign with the Cubs following the 2003 season, allowed eight hits and five runs in six innings.
Cubs first baseman Derrek Lee, who leads the majors with a .378 average, left the game in the third inning with irritation in his left shoulder and will be examined Wednesday.
Marcus Giles was 3-for-4 with three RBI, including a two-run double in the Braves' four-run fifth.
In the seventh, the Cubs loaded the bases on singles by Aramis Ramirez, Todd Hollandsworth and Henry Blanco. With one out, Colon struck out pinch-hitter Jose Macias and then ended the inning on a fly ball by Neifi Perez.
"I definitely think the guy today was Roman," Giles said. "He just tightened up his belt a little bit in that situation and that shows you a lot about him."
The Braves (47-37) moved 10 games over .500 for the first time this season. Atlanta has won four of five and 14 of 19.
Maddux, who won three Cy Young Awards with the Braves from 1993-2003, received a loud ovation when the starting lineups were introduced before the game and again before his first at-bat in the third inning.
"That was nice," he said. "It's nice not to be forgotten. I enjoyed that.
"I left here on good terms. I'm grateful for what the Braves did for me. They treated me great, paid me good and let me do my thing."
After facing only one batter, Maddux already was being visited by manager Dusty Baker, who wanted to make sure the 39-year-old was OK after having Rafael Furcal lead off with a shot that bounced off Maddux to Perez at shortstop. Perez threw out Furcal.
"I should have caught it," said Maddux, who said the ball hit his glove. "I whiffed."
Kelly Johnson followed with a double to center that Corey Patterson misplayed, taking a step in before watching the ball sail over his head. Johnson scored when Giles followed with a single up the middle for a 1-0 lead.
Hollandsworth's fifth homer pulled the Cubs even in the second.
Maddux gave up a leadoff double to Johnny Estrada in the second and then retired 10 straight batters. During that span, Maddux recorded six strikeouts, five on called strikes.
But the Braves reached Maddux for four runs in the fifth, all scoring with two outs.
With one out, Wilson Betemit reached on an infield single and moved to second on Colon's sacrifice bunt. After a walk to Furcal, Johnson's single to center drove in Betemit. Giles drove in two runs with a double to center, and Jones' single -- the third straight hit to center -- scored Giles for a 5-1 lead.
"He was good except for that one inning," Baker said of Maddux. "We've got to stay out of that big inning."
- Jones was thrown out by Blanco trying to steal second on a pitchout by Maddux in the fifth. Jones has two steals and has been caught twice.
- The Cubs lost seven straight games from April 29-May 7.
- Hollandsworth, who had two hits, has an eight-game hitting streak.