Soriano was booed by Cubs fans after he stood and watched a long fly ball hit the left-field wall for a long single in the eighth. Soriano didn't run to first, apparently thinking the ball would clear the fence.
He was stranded on third base when the inning ended.
"I apologized to him and I apologized to my teammates," Soriano said after speaking with manager Lou Piniella. "I said that's not going to happen again."
Watching possible homers without running has been an issue throughout Soriano's big-league career. He was criticized by the New York Yankees following the 2001 AL Championship Series opener for failing to run out a ball he thought was a home run against the Seattle Mariners and getting only to first base when it clanked off the wall.
"I talked to Alfonso about it, and I told him that he's one of our leaders here and there's no reason for that," Piniella said. "He apologized and said it won't happen again. Over."
Soriano's pose at the plate may have prompted Braves left-hander Francisley Bueno, who made his major-league debut, to throw a pitch behind Soriano's head in the ninth. Bueno was immediately ejected by plate umpire Ed Rapuano.
"We've got pitchers who can do that to the other team, too," Soriano said. "They do that to us, why can't we do that to them?"
Soto hit a two-run homer off Bueno earlier in the ninth.
"That's part of the game," Soto said of the pitch behind Soriano's head. "You have to live with that stuff. It's been around since the beginning of the game."
By stretching a road winning streak to six for the first time since May 17-June 2, 2005, the NL Central leaders improved their road record to 27-30. The Cubs swept three games from the Braves at home from June 10-12 and have outscored Atlanta 30-11 this season.
Chicago (72-47) moved 25 games over .500 for the first time since ending the 1984 season at 96-55.
Marquis (8-7) gave up two runs and six hits in 5 1/3 innings for his first win against Atlanta, his first major-league team. Marquis was 0-3 with a 14.04 ERA in his first four starts against Atlanta the Braves.
Braves manager Bobby Cox was ejected by third base umpire Joe West in the top of the fifth. Cox never left the dugout but complained when West halted play for the lights to be turned on after Braves reliever Vladimir Nunez warmed up. Cox has been ejected a record 142 times, including seven this season.
Cox said West said he wanted the lights on for a complete inning, giving each team's batters the same lighting on a cloudy day. West asked for the lights to be turned on in the fourth, but when they were slow to come on, Piniella asked for the lights to be turned off later in the inning, causing a delay.
Charlie Morton (3-6) gave up four runs and four hits in 2 1/3 innings.
Soto, who was 3-for-5 with four RBIs, hit a two-run double in the second against Morton and a two-run homer in the ninth off Bueno.
Edmonds hit a two-run, opposite-field homer to left in the third and had an RBI in the three-run fifth.
Right fielder Kosuke Fukudome was 0-for-4 with a walk for Chicago and is 3-for-32 (.093) in August. ... The Cubs drew six walks and lead the majors with 468. ... Morton is 0-5 with a 9.00 ERA in six home starts.