Scott Moore singled to left field, scoring Altuve and bringing his teammates storming out of the dugout for the second time in as many nights as they secured a 6-5 victory at Minute Maid Park.
"When you don't do it all season and you do it in back-to back nights, that's really nice and obviously everybody enjoys that," manager Brad Mills said.
The Astros, wearing throwback jerseys by choice since they won in them in walk-off fashion on Friday, hadn't won back-to-back games since June 26-27 against the Padres. The win also secured the Astros' first series victory since winning two of three against Cleveland from June 22-24.
Mills said his players immediately asked to wear the throwback jerseys again for Sunday's series finale. The Astros must check with the league office and the Brewers before being able to wear the uniforms for the third straight day.
Trailing 5-4 after eight innings, the Brewers rallied in the ninth to tie the game against closer Wilton Lopez.
Rickie Weeks led off the ninth with a double, moved to third on an infield single by Jonathan Lucroy and scored on a groundout by Jean Segura. Lopez struck out Martin Maldonado and retired Norichika Aoki to end the ninth.
Carlos Corporan, Ben Francisco and Tyler Greene all struck out in the ninth to send the game to extra innings. Lopez came back out for the 10th and allowed a two-out single, but struck out Corey Hart to give the Astros another chance.
They seized the opportunity. Moore, who had popped up with a runner at third and less than two outs twice already in the game, swung hard and missed badly on Henderson's first pitch.
"I swung through it but still had two more strikes to work with," Moore said. "The pitch that I put in play was probably a little outside but it was lower in the zone and easier to handle. I was able to get it over the infield. It kind of worked out."
Mills said the team's mentality in recent days shined through in Moore's final at-bat.
"The first [pitch], it looked like the train was in danger," Mills said. "And then he came back and just did what he had to do, put the ball in play and served it in and won the game. He did an outstanding job."
Greene made an impact early in his first start for the team, doubling down the left-field line on the third pitch from starter Marco Estrada.
"It definitely helped me relax the rest of the game," Greene said.
Altuve singled and Pearce brought both runners home with a single to give the Astros an early two-run lead.
Altuve, who finished with three hits, scored again in the third after singling, stealing second base and racing home on Brett Wallace's single to right field. Pearce, with three hits himself, tripled to score Wallace.
Estrada lasted just four innings, giving up four runs on seven hits.
"I just felt completely out of whack out there," Estrada said. "That's the worst I've felt all year. I let a bad team beat me."
Greene added a solo homer, his fifth of the season, off reliever Livan Hernandez in the fifth.
Starter Dallas Keuchel and the Astros' bullpen kept the Brewers' bats in check for most of the evening.
In his ninth career start, Keuchel pitched well early on. Wallace's throwing error helped the Brewers score two unearned runs in the second, but the left-hander retired the Brewers in order in the first, third and fourth.
He ran into some trouble in the fifth after Lucroy doubled and Segura singled with one out. Aoki made Keuchel pay, doubling to center field to tie the game at 4.
Keuchel was lifted for for reliever Chuckie Fick after tossing a scoreless sixth. He struck out a career-high six and walked none, a career-best, with 77 pitches.
"I was able to command the ball today and it showed," Keuchel said.
Fick struck out the first two batters of the seventh before Segura singled. Against reliever Wesley Wright, Travis Ishikawa and Aoki reached on infield singles to load the bases. Mickey Storey, who replaced Wright, struck out Carlos Gomez looking with a breaking ball at the knees to end the inning.
Gomez was ejected from the game after arguing the call with home-plate umpire Gary Darling.