Yordan Alvarez and Martín Maldonado also went deep to help Houston split the four-game series, the first meeting between the teams since the Astros swept the ALCS last October.
Houston, which holds an AL wild-card spot, remained 2 1/2 games behind first-place Texas in the AL West.
“Just didn’t seem like that game was going to end,” Astros manager Dusty Baker said. “We helped them, they helped us. Hard-fought victory for us.”
Jeremy Peña scored twice for the Astros, who have won 11 of their past 15 matchups with the Yankees - including last year's playoff series.
Gleyber Torres homered and reached base five times. Harrison Bader also had three hits and two RBIs for the fourth-place Yankees, who fell 4 1/2 games behind Toronto for the final AL wild card.
Rodón was removed in the third inning with left hamstring tightness and replaced by rookie Jhony Brito.
After being examined at Yankee Stadium by a doctor, Rodón will get additional tests in the next 24 hours, the team said. New York manager Aaron Boone was unsure if Rodón would require another stint on the injured list.
“We’ll have an MRI tomorrow and then we’ll have an idea,” Boone said.
Signed to a $162 million, six-year contract in the offseason, Rodón missed the first three-plus months of the season with a forearm strain and a bad back. The 30-year-old left-hander has been a disappointment since, allowing four earned runs or more in four of his six starts.
He struggled against the Astros, giving up five runs over 2 2/3 innings - including homers to Meyers and Alvarez. Rodón struck out five but has a 7.33 ERA in 27 innings this season. He was 2-0 with a 1.55 ERA in seven prior starts versus Houston.
“I’m pretty frustrated,” Rodón said. “This is not the way I wanted to come out here and perform.”
Meyers took Rodón deep to left-center after a pair of walks in the second. Meyers then put Houston in front for good in the sixth with a 432-foot drive off Wandy Peralta (3-2) for his second career multi-homer game.
“That was big,” Baker said. “He’s been making some adjustments, trying to find his stroke, and he found it on two of them.”
The six RBIs for Meyers matched the most by an Astros player this season. The 27-year-old center fielder noted it was the first time he could recall driving in that many runs in a game at any level.
“It was a really fun game to be a part of,” Meyers said. “An absolute battle. Glad we won.”
Maldonado followed with a drive to left field to make it 9-5, marking the ninth set of back-to-back homers for Houston this season. The normally reliable Peralta, who served up a long ball Thursday to Kyle Tucker, has allowed homers in consecutive outings for the first time this year.
“Today I wanted to execute every pitch,” Peralta said through a translator. “Things didn’t work out the way that I wanted it and unfortunately it cost (us) the game.”
Torres barely clearly the right-field wall in the first, connecting off José Urquidy for his 18th homer of the season.
Urquidy settled down after that before losing the strike zone in the fourth, when he threw eight straight balls to load the bases. Urquidy was activated from the 60-day injured list before the game to make his first start since April 30. He had been sidelined with right shoulder discomfort.
Rookie right-hander J.P. France (8-3), making his first career relief appearance, did not allow an earned run in 3 1/3 innings.
“It was definitely different,” he said. “But at the end of the day, you still have to go out there and give your team a chance to win.”
Bryan Abreu got four outs for his fourth save. Giancarlo Stanton flied out to Meyers with two on to end it.
“At the end, it was tough,” Meyers said. “It went into the sun and then came out and it was fun to catch the last one.”
Yankees slugger Aaron Judge went 0 for 4 with an RBI and is 5 for 27 since returning from a toe injury.
Astros: After having Saturday off, closer Ryan Pressly was unavailable due to soreness, Baker said. He did not provide any other details.
Yankees RHP Jonathan Loáisiga (elbow inflammation) is expected to be activated from the injured list before Monday’s game at the Chicago White Sox. Loáisiga, sidelined since April 8, made three minor league rehab appearances.
Astros: Houston is scheduled to visit the White House on Monday to mark its 2022 World Series championship. LHP Framber Valdez (9-7, 3.07 ERA) takes the mound one day later in the opener of a three-game series at AL East-leading Baltimore. Valdez threw the 16th no-hitter in team history last time out, beating Cleveland 2-0. RHP Grayson Rodriguez (2-3, 6.09) starts for the Orioles.
Yankees: RHP Gerrit Cole (10-2, 2.64 ERA) opens a three-game series Monday in Chicago. Cole leads the AL in ERA. RHP Dylan Cease (4-5, 4.61) goes for the White Sox.
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