Gausman was tossed in the second inning for throwing a 97 mph fastball behind Urena. Touki Toussaint (2-0), recalled from Triple-A Gwinnett, replaced Gausman and allowed one run in four innings with six strikeouts.
"It's a special win," Toussaint said.
"Things happen during a game," Braves manager Brian Snitker said. "We just kind of refocused and got back to work."
Urena (1-5) allowed five runs in six innings. He said Gausman's inside pitch set a bad example for the fans.
"That's the way they claim they are professional?" the Dominican said in Spanish. "I've never had anything against them. They are the ones keeping it going."
Marlins manager Don Mattingly was asked if the feud between the two NL East teams is over.
"We'll see," he said.
Freeman hit his sixth home run in the first inning. He has 26 career homers versus Miami, the most he has hit against any team.
McCann hit a sacrifice fly in the fourth and a two-run homer in the sixth, his second. Josh Donaldson, back in the lineup after missing three games with a calf injury, contributed three hits and three RBI.
Gausman's first pitch to Urena was knee-high behind the batter, and plate umpire Jeff Nelson immediately signaled the ejection.
"He was ejected for intentionally throwing at the batter," Nelson said.
The game was Urena's first against the Braves since he was suspended for six games for intentionally hitting Atlanta's Ronald Acuna Jr. on the arm with a pitch last August, triggering a bench-clearing confrontation.
Nelson declined to say whether that history was a factor in the ejection, but Snitker said that was part of the umpires' rationale.
"You don't have to agree," Snitker said. "They're doing their job the best they can."
No warnings were issued before the game, but Gausman didn't complain about being tossed for throwing behind Urena, either.
"Obviously the umpires thought there was a reason behind it, and decided to throw me out," Gausman said.
Five Braves pitchers combined on a six-hitter against the Marlins, who are last in the majors in runs.
After Gausman departed, there was no further escalation of tension between teams. But Mattingly was ejected by Nelson in the sixth inning for arguing balls and strikes.
Before the game, the Marlins recalled from rehab and reinstated RHP Austin Brice (gastroenteritis) and optioned LHP Jarlin Garcia to Triple-A New Orleans.
Braves: RHP Mike Soroka (2-1, 1.62) is scheduled to make his fourth start Saturday.
Marlins: RHP Trevor Richards (0-4, 4.64) is winless in six starts even though opponents are batting .218 against him.
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