Roundly booed by Cubs fans in his first season in 2004, he became a fan favorite the next year by leading the National League with a .335 average with 50 doubles, 46 home runs and 107 RBI, the Chicago Tribune reported.
Lee was a contributor in 2007 and 2008 when the Cubs made the playoffs before back-to-back October disappointments.
The Braves gave up three low-level pitching prospects to get Lee and will have to pay him $1.7 million, half his remaining salary.
Lee rejected a trade to the Los Angeles Angels three weeks ago, saying the "timing" wasn't right.
But the Cubs' season went into free fall, and an injury to Chipper Jones brought Atlanta calling.
"I understand what Jim (Hendry) is trying to do over here," Lee said of Atlanta. "It just felt right, and the chance to go to the post-season, it's hard to pass up."
"I had a great time (in Chicago)," he said. "I grew as a player, as a person. We didn't achieve the ultimate goal. Coming in here it seemed like we were going to win a championship, so that part's disappointing. The rest of my experience was nothing but positive."