Once Brewers pitching coach Rick Kranitz told him in the middle of the first inning to take less time between pitches, Estrada found the perfect rhythm.
"I felt good with the fastball early, but the off-speed pitches weren't there," Estrada said. "I think it was because my tempo was too slow. So I picked it up, picked up the pace. The changeup was coming out a lot better after that."
The NL East champion Braves began the night with the league's best record and are one-half game in front of St. Louis Cardinals, who beat Washington 4-3 on Monday. The Los Angeles Dodgers, who did not play Monday, moved two games back.
Gomez gave Milwaukee a 1-0 lead in the first, hitting the first pitch he saw from Mike Minor (13-8) for his 22nd homer.
The Brewers went up 3-0 in the fifth when Norichika Aoki doubled and scored on Lucroy's 18th homer.
Estrada (7-4) gave up two hits, walked three and struck out six. He threw a career-high 115 pitches, 76 for strikes.
"I thought Marco threw the ball outstanding," Milwaukee manager Ron Roenicke said. "His changeup was great, located his fastball well and threw some nice curveballs. When he has that changeup going, he's capable of throwing this against anybody."
Minor allowed eight hits and three runs and struck out six in seven innings. The left-hander, whom manager Fredi Gonzalez is considering to start Atlanta's playoff opener next week, is winless in his last five starts.
In his last eight starts since coming off the disabled list with a strained left hamstring, Estrada is 3-0 with a 2.26 ERA, a span of 51 2/3 innings. He improved to 3-1 and lowered his ERA 1.54 points to 3.96 in four career starts against Atlanta.
"It's always my goal to at least go seven, and if you can, go more," Estrada said. "I know my pitch count was a little high by then. Ron asked me how I felt. I told him, `I'm good. I've got at least one more inning.' And he gave it to me. So I knew he had some trust in me."
Estrada pitched out of trouble in the fourth. Leading 1-0, he walked Jordan Schafer and Upton. Chris Johnson, the next batter, struck out on a wild pitch that moved the runners up, but Estrada struck out Evan Gattis and Simmons.
After Ramirez's 12th homer in the eighth, Milwaukee took a 5-0 lead when Sean Halton doubled off Varvaro, moved to third on Yuniesky Betancourt's infield single and scored on shortstop Simmons' throwing error.
Minor has allowed at least two homers in seven starts this season and is 0-3 with a 5.12 ERA in those outings.
"I went seven innings, kept us in the game and gave us a chance to win," Minor said. "Those are the positives I take out of it. Also, the negatives are two home runs. Can't keep the ball in the yard, so I'll try to fix it."
Home plate umpire Angel Hernandez ejected Gonzalez with two outs in the seventh. With a runner at first, Estrada hit Paul Janish in the left leg with a pitch, but Hernandez ruled that Janish, who leaned into the 89 mph fastball, did not attempt to get out of the way.
Gomez began the night 11 for 35 with two homers and 12 RBIs in last 10 games, but struck out four times after hitting the homer. ... 1B Freddie Freeman, the first Atlanta player with at least 100 RBIs since Chipper Jones and Jeff Francoeur in 2007, was given the night off. Freeman has hit safely in 16 of his last 19 games with six homers and 17 RBIs. ... Roenicke said SS Jean Segura, out since last Wednesday with a strained right hamstring, did some running Monday and could be used off the bench by Wednesday. ... The Brewers snapped an eight-game losing streak at Turner Field.