Gausman was tossed in the second inning for throwing a 97 mph fastball behind Urena. Touki Toussaint, recalled from Triple-A Gwinnett, replaced Gausman and allowed one run in four innings with six strikeouts.
"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?'' he said through an interpreter. "I've never had anything against them. They are the ones keeping it going.''
Marlins manager Don Mattingly, who was ejected in the sixth inning for arguing balls and strikes, was asked if the feud between the two NL East teams is over.
"We'll see,'' he said.
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 in August, triggering a bench-clearing confrontation.
Nelson declined to say whether that history was a factor in the ejection, but Snitker said it was part of the umpire's 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.
"Obviously, the umpires thought there was a reason behind it and decided to throw me out,'' Gausman said.
The Associated Press contributed to this report.