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. Omar Infante, who was preparing to face Buchholz at the plate, never saw a pitch.
Julian Tavarez (1-2) earned the victory with a scoreless 10th inning.
Buchholz (6-6) lost for the third time in his past five appearances. He had two out when Johnson singled and moved to third on Josh Anderson's double.
Colorado, which last year earned their first NL pennant by going 21-1 after Sept. 16, has lost three in a row and four of five. The Rockies began Tuesday six games behind Los Angeles in the NL West. The Dodgers were playing late in San Diego.
Atlanta, which ended a two-game losing streak, had lost 20 of 27.
Brian McCann's RBI single and Casey Kotchman's two-run single gave the Braves a 3-0 lead in the first.
Brad Hawpe's 24th homer, a two-run shot off Atlanta starter Jorge Campillo, cut the Braves' lead to 3-2 in the fourth.
After the Braves took a 4-2 lead in the sixth on Jeff Francoeur's RBI double, Chris Iannetta hit his 15th homer, also off Campillo, in the seventh.
Garrett Atkins' 19th homer forced a 4-all tie in the ninth off Braves closer Mike Gonzalez, who blew his first save since June 25, 2004 and end the majors leagues' longest active streak at 39.
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 past six starts.
Kotchman had two golden opportunities to give Atlanta a big lead late and flied out to center in the seventh and grounded into a double play in the ninth. Both times the bases were loaded.