Marquez had a no-hit bid going until Kris Bryant's double leading off the seventh inning. He walked Kyle Schwarber in the first and retired 16 straight before Bryant's hit to left.
The 22-year-old Marquez (1-2) struck out eight by mixing in a mid-90s fastball with an assortment of breaking pitches. With two on and two outs in the seventh, Marquez broke opener the game with his liner to left. The Rockies bench gave him an ovation.
Greg Holland threw a perfect ninth for his 14th save in as many chances to help the Rockies take two of three from Chicago.
Kyle Hendricks (2-2) gave up three runs -- two earned -- in 6 1/3 innings.
Marquez was recalled from Triple-A Albuquerque on April 25 to fill in for injured Jon Gray. He struggled in his first two starts at Coors Field this season, posting an 11.70 ERA.
He found his electric stuff Wednesday after a rain delay of 50 minutes at the start. It's the sixth time a Rockies pitcher has thrown at least six innings of no-hit baseball at Coors Field and first since Jorge De La Rosa on May 16, 2014, according to Elias Sports Bureau.
Marquez found himself in a tight spot in the eighth with two on and one out. Manager Bud Black showed faith in him to escape and he did, too, by getting two groundouts to end the threat.
Cubs: SS Addison Russell was a late scratch with soreness in his right shoulder.
Rockies: C Tony Wolters (concussion) is taking swings in the batting cage. "There are no symptoms. I feel good, I feel like a normal human being. Ready to get out there," Wolters said. ... With his foot on the bag, Reynolds was stepped by pinch-hitter Willson Contreras in the eighth as he ran down the line. Reynolds stayed down for a moment but remained in the game.
PUT HIM IN, COACH
Third base on Tuesday, first base on Wednesday -- Jeimer Candelario doesn't care where he plays. He was recalled from Triple-A Iowa on Tuesday as the 26th player before the second game of a doubleheader, but was kept around. Instead, pitcher Dylan Floro was sent back to Triple-A Iowa.
"It's about doing the job," said Candelario, who was hitting .340 at Iowa. "Right now, got to be able to concentrate, get my job done and help the team win."
A slumping Trevor Story was out of the starting lineup Wednesday. The shortstop is hitting .180 with six homers and 15 RBI. This after hitting 27 homers last season before going on the DL in August with a torn ligament in his left thumb.
He's trying to recover that version of his swing.
"A lot of time it has to happen through time," Black said.
Cubs: Off Thursday before a three-game series in St. Louis. Maddon has yet to announce a start for Friday's game.