Flores hit a two-run shot off Hayden Wesneski (1-1) after Lewis Brinson walked for his 18th homer of the season, matching a career high and snapping an 0-for-19 skid.
Estrada led off the seventh with his 13th of the season. The homer ended Wesneski’s streak of six scoreless innings to begin his major league career.
Seiya Suzuki homered off Scott Alexander in the eighth to pull the Cubs within 4-2.
“The consistency he’s produced for us for a month-plus now has been really solid,” manager David Ross said of Suzuki. “I think this is the player we thought he was.”
Left-handed starter Wade Miley gave up a run and four hits, struck out five and walked one in five innings for the Cubs. It was his second outing after missing three months with a shoulder injury.
“It’s huge for me to prove that I’m healthy and I can still compete at a high level,” Miley said. “Obviously, every time I go out I want to give us a chance to win and keep our team in the game. Selfishly, it’s very important I can prove I can still pitch here.”
Zack Littell (3-3) threw 1 2/3 shutout innings to earn the victory. Camilo Doval worked around a hit batter and a triple in the ninth, pitching 1 1/3 scoreless innings for his 22nd save.
“I just told him I wanted him to pick the pace up a little bit and just let it go, throw everything for a strike,” Bart said of his mound visit.
“I told him after the game, ‘Saves pay a lot of money, man. You want that ball and you want that save at that time,’ ” Bart added.
John Brebbia allowed a hit in a scoreless first inning as the Giants opener. San Francisco relied on its bullpen to fill in for Alex Wood, who went on the 15-day injured list with a shoulder injury on Sept. 3.
“Our bullpen overall did a nice job of attacking the zone,” Giants manager Gabe Kapler said.
J.D. Davis doubled off Miley and scored on Estrada’s two-out single for a 1-0 Giants lead in the fourth.
The Cubs tied it in the fifth. McKinstry doubled off Yunior Marte and scored when Rafael Ortega singled and advanced on right fielder Luis González’s fielding error.
SOGGY NO MORE
No rain fell during the game, which started a few hours after the Chicago Bears beat the San Francisco 49ers 19-10 at a rain-soaked Soldier Field.
Cubs DH Franmil Reyes was shown on the ESPN broadcast singing Whitney Houston’s “I Will Always Love You” in the dugout.
Giants: C Austin Wynns was available off the bench for the second straight game after he was struck in the head by a Drew Smyly pitch on Friday.
Cubs: SS Nico Hoerner (right tricep tightness) exited after trying to make a diving play in the fifth inning. … 2B Nick Madrigal (right groin strain) said he hopes to return before season’s end but knows he has to be smart about the injury. He went on the 10-day IL Saturday. Madrigal said he plans to make “major changes” after dealing with injuries the last two seasons. “If it’s not feeling right, I’m probably not going to get in there,” he said. “So I’d love to, but we’re going to have to see how it goes.”
Giants: RHP Alex Cobb (5-6, 3.68 ERA) will start Monday to begin a homestand against the Atlanta Braves and RHP Spencer Strider (10-4, 2.69).
Cubs: RHP Javier Assad (0-1, 2.93) is scheduled to start Monday at New York. RHP Chris Bassitt (13-7, 3.24) is slated for the Mets.
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