CHICAGO -- Wily Peralta initially couldn't decide what was the bigger highlight on Sunday - an RBI base hit or repeatedly pitching his way out of tough situations.

"Both," Peralta said with a laugh following the Milwaukee Brewers' 3-1 victory over the Chicago Cubs. "No, I think being able to make good pitches when I had to. I got a lot of people on base today, but when I had to make a pitch, I was able to execute."

Peralta (7-10) worked six innings for the victory and faced runners in scoring position in five of them. He held Chicago (94-55) scoreless until the sixth.

He also went 1-for-2 with a second-inning base hit to score catcher Martin Maldonado.

Right-handed reliever Tyler Thornburg earned his 11th save despite putting two Cubs on base in the ninth. He struck out Kris Bryant and Anthony Rizzo to preserve the win.

The Brewers (68-82) took three of four from the Cubs and improved to 11-6 in September.

"We had a winning September road trip, 11 days and 17 straight games," Milwaukee manager Craig Counsell said. "The guys just keep doing it. It speaks to them finishing the season, finishing strong and continuing to play well and at a high level."

Cubs right-hander Kyle Hendricks (15-8) suffered his first loss in nine starts. The Cy Young Award candidate last lost on July 26 against the White Sox and then won six games and had two no-decisions over the next seven-plus weeks.

Hendricks said he didn't have full command of his pitches - especially his fastball.

"I had a good first inning, my command was kind of there but after that my fastball command kind of left," Hendricks said. "A couple of base hits in that (second) inning and they got a couple of base hits and that was really it."

Chris Carter added an insurance run as he slugged his team-leading 36th home run of the season off Cubs reliever Felix Pena in the eighth.

Carter closed to within one homer of Bryant, whose 37 homers are second in the NL.

Chicago fielded its normal starting lineup after manager Joe Maddon gave nearly all regular position players the last two days off.

The Brewers hit Hendricks for three straight base hits and two runs in the second as they opened a 2-0 lead.

Hernan Perez led off the inning with a single and Milwaukee delivered three straight singles with two outs to score Perez and Peralta.

After putting runners in scoring position in the second through five innings but failing to score, the Cubs finally broke the shutout in the sixth.

Javier Baez reached on a fielder's choice and came home on pinch hitter Tommy La Stella's two-out double to center to cut the deficit to 2-1.

"We just could not get it to fall in the right spots," Maddon said. "We were just unable to take advantage of opportunities. We had them."

That inning was also the end for Hendricks. He allowed two runs on six hits while walking two and striking out nine and throwing 97 pitches, 63 for strikes.

"I thought Kyle was really good," Maddon said. "(He) didn't have his best command of his stuff, but still (nine strikeouts) that tells you what's going on with his movement."

Peralta also worked six innings, giving up one run on nine hits while walking one and striking out five.

"His best pitches came with runners on base and then in big spots," Counsell said. "So there was some traffic for sure but when there was traffic that's when the high execution came."

Sunday's game was the 19th and final meeting of the season between the teams.

NOTES: Milwaukee OF Ryan Braun had the day off after a 3-for-5 performance on Saturday that included a pair of two-run homers as he reached 30 for the season. Since 2007, Braun has 29 homers against the Cubs. He also has 107 RBIs versus Chicago, more than any other active player. ... The Brewers have Monday off before starting their final homestand of the season -- a six-day run that features a three-game series with Pittsburgh. ... Milwaukee sends RHP Matt Garza (5-7, 4.22 ERA) against a Pirates pitcher to be named. ... Chicago resumes its final homestand of the season on Monday with the first of three game against the Cincinnati Reds. The Cubs send RHP Jason Hammel (14-9, 3.60 ERA) against Reds RHP Tim Adleman (2-4, 4.21 ERA). The Cubs complete the week against the St. Louis Cardinals and then hit the road to close the regular season. ... Chicago's division clincher last week came in its 146th game, the fewest the team has needed to win since divisional play began in 1969. It was also the earliest clinching by any Central team since the division was created in 1994.