Either way, Atlanta's offense struggled again, and the Braves lost a critical three-game series to the Milwaukee Brewers.
"It's a tough game and unfortunately I got kicked out in the first inning for doing nothing," Freeman said. "It's a little frustrating."
The NL East champion Braves were shut out for the second time in three games, falling 4-0 on Kyle Lohse's two-hitter Wednesday night.
After losing three of four, Atlanta (93-65) has fallen two percentage points behind the St. Louis Cardinals (94-65) for the NL's best record.
Lohse (11-10) struck out five and threw just 22 of 89 pitches for balls. In his first season with Milwaukee, Lohse was pitching for St. Louis when he had his last shutout, a 5-0 victory over Washington on April 21, 2011.
Gomez, made it 1-0 in the first with his 23rd homer, but was ejected without touching home plate during a benches-clearing argument.
Freeman, Atlanta's best hitter, was ejected along with reserve catcher Gerald Laird.
Gomez, the Brewers' top slugger, stirred emotions on both teams as the game's second batter.
As soon as he homered, Gomez stood in the batter's box watching the ball sail into the seats in left field, stared at Maholm and flipped his bat behind him.
Gomez, who was yelling at Maholm as he slowly trotted up the first base line, was still upset that the pitcher hit his leg with an 88 mph fastball in the Brewers' 7-4 home loss to Atlanta on June 23.
"I don't apologize for this," Gomez said. "Just take the pain back. You can see the replay. They hit me for no reason, and I tried to get it back today. It's the only opportunity that I have. That's what I did."
The argument continued as Gomez slowly trotted across first and began jawing with Freeman, who said he told Gomez to "act like he'd been here before" and run the bases.
"If you have a beef with the pitcher, have a beef with the pitcher," Freeman said. "Don't make us get involved. That's us. We're going to back up our pitcher. I'm fine with how everybody handled it."
Gomez touched second and third without incident before Brian McCann, Atlanta's catcher, stood in the third base line about 20 feet from the plate and stopped him.
The benches emptied, and Gomez was ejected for shoving Braves reserve outfielder Reed Johnson and Freeman for pushing a pile of players and coaches.
Dana DeMuth, the third base umpire and crew chief, didn't hesitate to eject Freeman.
"Right when he came in, he went boom with an elbow, which we saw, and it caught the third baseman, [Aramis] Ramirez," DeMuth said. "That right there is just like throwing a punch. That is overaggressive. That, No. 1, calls for an ejection. What we saw out there was the same as we saw [on video]. There was nobody else that was overly aggressive other than Gomez, of course."
Gomez never touched home plate, but the Brewers were still credited with a run because McCann was charged with obstructing the runner.
DeMuth added that Laird was ejected for arguing from the dugout after the game restarted.
Logan Schafer took Gomez's spot in center field. Chris Johnson took Freeman's spot at first while second baseman Dan Uggla entered the game for Atlanta and Elliott Johnson moved from second to take Johnson's spot at third.
One run was all Lohse needed. He retired 20 straight batters after Andrelton Simmons led off the first with a bunt single, and threw just 54 pitches, 42 strikes, through the first six innings.
Lohse is 10-4 with a 2.91 ERA over his last 22 starts. He pitched his 10th career complete game, allowing four hits, two starts ago in a 5-1 home victory over Cincinnati on Sept. 13.
"I felt good to go out there and establish that I was going to throw strikes," Lohse said. "And they were swinging so the end result of that is if you've got a good defense behind you you're going to have a decent game. And that was a little bit better than decent."
Evan Gattis' two-out single in the seventh gave the Braves their second and last baserunner, but McCann followed with a flyout.
All three runs were charged to Maholm (10-11), who gave up eight hits and struck out seven in seven innings.
Scott Downs, the third Atlanta pitcher, gave up an RBI single to Aoki with one out in the ninth to make it 4-0.
Lohse, facing Atlanta for the first time this season, began the night 3-1 with a 4.97 ERA in 10 career starts against the Braves.
Maholm, who dropped to 5-11 with a 5.07 ERA in 24 career starts against Milwaukee, was shocked at Gomez's antics.
"When he rounded third and was still acting like that, I told him, 'Congratulations, you hit a homer. Run,'" Maholm said. "That's all I said. Like I said, he's not the first and he's not the last to hit a homer off me. He's probably not going to be the last guy that pimped it. You can pimp it and do whatever, but at least run the bases."
Gomez didn't blame McCann for blocking his path to the plate.
"If I'm a catcher, I do the same thing," Gomez said. "I try to protect my pitchers, my teammates. I respect McCann, all his players. I'm going to apologize to his manager, his organization, that it went that far. The adrenaline, the emotion takes it more than you expect."
Betancourt entered the game when Ramirez left midway through the third inning with left knee soreness. ... Gonzalez confirmed before the game that RHP Brandon Beachy will not pitch again this season. On the DL since Aug. 23, Beachy is 2-1 with a 4.50 ERA in five starts this year after missing 105 games to recover from elbow ligament replacement surgery. Gonzalez said Beachy hasn't had a setback, but added that the team wants him fully healthy for the start of spring training. ... Rookie RHP Jimmy Nelson will make his first career start when the Brewers visit the New York Mets on Saturday. Nelson, who made his debut on Sept. 6 at the Chicago Cubs, has pitched three scoreless innings in five games this season. ... Nelson is taking the place of RHP Wily Peralta. Milwaukee manager Ron Roenicke said Peralta, who went 11-5 with a 4.37 ERA in 32 starts, has a blister on his right index finger and needs to rest. ... Brewers SS Jean Segura still wants to return for the final weekend, but was unable to run in the outfield before the game because of the wet field. Segura has been sidelined since Sept. 25 with a strained right hamstring.