Lee, batting with the bases loaded and one out, lined a shot off Juan Gutierrez (0-3) past diving third baseman Mark Reynolds to drive in pinch-runner Tyler Colvin and Ryan Theriot and break a 5-5 tie.
Lee ended the game 2-for-5 with a run scored while Kosuke Fukudome doubled twice, walked and drove in a run for Chicago.
Sean Marshall (1-1) earned the win with two scoreless innings of relief, while Carlos Marmol got his fourth save despite a shaky ninth, during which he loaded the bases with two walks and a hit.
Reynolds belted two homers -- his eighth and ninth of the season -- for the Diamondbacks, who dropped their second straight in a three-game series at Wrigley Field.
2014: The Year in Music [PHOTOS]