ATLANTA -- Taylor Buchholz chalked up this loss to confusion.
"I took the sign, something I've done dozens of times," Buchholz said. "I was going to throw a curveball. I got the grip, and I don't know what happened."
Buchholz, pitching from the stretch, had already moved his feet to begin his windup when he paused, apparently wanting to restart the pitch.
Home plate umpire Wally Bell instantly threw up his arms and waved home Johnson for the winning run.
Omar Infante, who was preparing to face Buchholz at the plate, never took a pitch in the at-bat.
"As soon as I did it, I knew it was a balk," Buchholz said. "I'd rather they beat me with a hit."
Colorado, which last year earned its first NL pennant by going 21-1 after Sept. 16, has lost three straight and four of five. The Rockies began Tuesday six games behind Los Angeles in the NL West.
Atlanta, which ended a two-game losing streak, had lost 20 of 27.
Julian Tavarez (1-2) earned the victory with a scoreless 10th inning.
Buchholz (6-6) lost for the third time in his last five appearances. He had two out when Johnson singled and moved to third on Josh Anderson's double.
"We won a game on a balk once, but it wasn't a walkoff balk," Rockies manager Clint Hurdle said. "We scratched and clawed. We were down three runs, then got back in it. We were talking a tightrope most of the way. I still thought we'd find a way to win it."
The Rockies scored all their runs on homers.
"It was fun while it lasted," Gonzalez said. "Now I've got to start another streak."
Rockies starter Aaron Cook allowed four runs and six hits in six innings. Since winning 7-4 at Pittsburgh on July 30, Cook is 2-3 with a 6.93 ERA in his last six starts.
Kotchman had two golden opportunities to give Atlanta a big lead late in the game, and failed both times.
In the seventh, he came up with the bases loaded and two outs against Glendon Rusch, and flied out to center.
In the ninth, Kotchman came up with the bases loaded and one out and the game tied, and grounded into a 6-4-3 double play.
"That's how we've been losing games, lining into double plays," Braves manager Bobby Cox said after his team improved to just 8-27 in one-run games. "It's happened all year, honestly, where a game-changer is hit right at somebody. We've played so many tight ones. We'll take anything, a walkoff balk or anything right now."
"The momentum switch just didn't happen," Tulowitzki said. "We had our chances. We didn't execute."
- Braves 3B Chipper Jones went 2-for-4 to boost his average one point to .359, and trails St. Louis' Albert Pujols, who also went 2-for-4, by two points for the best average in the majors.
- In his last 23 road games, Hawpe is hitting .383 in 86 at-bats.
- Cook missed on his second chance to win his 17th game, which would tie Jeff Francis (2007), Pedro Astacio (1999) and Kevin Ritz ('96) for most the franchise's most wins in a single season.
- The Rockies had three errors in a game for the first time since Sept. 2, 2006.