Chicago won its seventh straight game behind a stellar effort from Hendricks (8-7). He held Milwaukee without a baserunner until Martin Maldonado singled with one out in the sixth.
Maldonado grounded into a double play two innings later that allowed reliever Fernando Rodney to escape a first-and-third jam with one out.
Hector Rondon tossed a scoreless ninth for his 30th save.
The Cubs will face Pittsburgh in the wild card matchup on Wednesday. The Pirates needed to win one of their last two regular season games, or one Cubs' loss, to ensure that the postseason will start at PNC Park. The Pirates were playing Cincinnati on Saturday night.