Baez, who homered in his MLB debut on Tuesday, finished 3-for-4 with four RBI and two runs scored and Starlin Castro also homered for the Cubs, who earned their first series victory in Denver since sweeping a three-game set on Aug. 3-5, 2004.
Hendricks (3-1) surrendered just two runs on six hits and a walk with four strikeouts to earn the win.
Justin Morneau had two hits, an RBI and a run scored and Corey Dickerson also drove in a run for Colorado, which has dropped six of its last seven. Yohan Flande (0-4) gave up four runs on seven hits and a walk across six frames in defeat.
The Cubs opened the scoring in the second. Justin Ruggiano singled to left, moved to second on Welington Castillo's groundout and slid into home on Arismendy Alcantara's single to right.
Chris Valaika singled to lead off the third and moved to second on Hendricks' groundout. Two batters later, Baez hit an RBI single to left and moved to second on Dickerson's fielding error.
Hendricks retired the first nine batters before Charlie Blackmon's base hit to center opened the fourth. Blackmon took second on Josh Rutledge's flyout and scored on Morneau's double to deep left, making it a 2-1 game.
Nolan Arenado's bloop hit landed in front of Castro at short, who misplayed the ball to allow runners on the corners. Flande left the runners stranded by striking out Carlos Gonzalez and inducing an inning-ending flyout from Dickerson.
Baez and Castro led off the sixth by cranking back-to-back solo shots to left, giving the Cubs a 4-1 advantage.
In the home half, Morneau singled and Gonzalez walked with two outs before Dickerson's line drive to center plated Morneau to get the Rockies within two.
After Chris Coghlan walked to start the eighth, Baez smacked an 0-1 slider to right-center for his third home run of the series and a 6-2 lead.