The Rockies could have had more in the inning, but Alfonso Soriano threw out Todd Helton at home for the first out after a single by Josh Rutledge.
The Rockies added two more runs in the fifth on an RBI double by Troy Tulowitzki and run-scoring single from Helton. Colorado had three doubles to start the inning, including one from Dexter Fowler who was thrown out trying to stretch it into a triple.
Tulowitzki had three hits while Young, Helton, and Arenado had two apiece for the Rockies. Their 17 hits matched a season-high allowed by the Cubs.
Villanueava didn't think he was tipping off his pitches.
"Tipping, tippiing, chalk it up to I got hit."
Francis took a shutout into the fifth before Darwin Barney homered with two outs. Barney had three hits and two RBIs.
The Cubs scored two unearned runs in the eighth, first when reliever Edgmer Escalona fielded Anthony Rizzo's grounder but threw the ball into center field, allowing David DeJesus to score. Arenado then made a diving play on Soriano's grounder, but Starlin Castro came home to cut the Colorado lead to 7-3.
Colorado hasn't won a three-game series at Wrigley Field since Sept. 29-Oct. 1, 2006, when the Rockies took two of three.
NOTES: Roy Oswalt threw 64 pitches in an extended spring training start for the Rockies. He is scheduled to pitch again Saturday, and if that start goes well he is expected to join Double-A Tulsa. ... Rockies manager Walt Weiss said there hasn't been a decision made on whether Juan Nicasio will take his next start in the rotation. ... Cubs 3B Luis Valbuena was out of the lineup for the third straight day after suffering a jammed right pinky finger Saturday in Washington. Sveum said Valbuena will be in the lineup Wednesday in the finale of the three-game series. ... Wednesday's pitching matchup is Colorado's Jon Garland (3-3, 4.83) against the Cubs' Jeff Samardzija (1-5, 3.70).