The right-handers went at it for eight innings before Colorado added three runs against two relievers in the ninth for a 5-1 victory over Atlanta on Monday night.
The Braves dropped to 6-11 at Turner Field this season, and the latest loss was in front of 15,364, the smallest paid crowd since the stadium opened in 1997.
Marquis had the right strategy to keep Atlanta's hitters off balance.
"I pounded the bottom of the strike zone," he said. "I was able to attack the strike zone and put the ball on the ground."
Marquis (5-3) scattered five hits and allowed one run in eight innings to end a two-start losing streak. He struck out three and walked three.
Marquis gave up 16 runs -- 14 earned -- in his previous two starts, a span of 9 2/3 innings against San Francisco and Houston. Even so, the right-hander believes his talent doesn't match his career 4.56 ERA.
"I feel like every time I get the ball, I'm going to shut them down," Marquis said. "I'm out there every pitch battling."
Lowe (5-2) was attempting to become the NL's first six-game winner. He allowed two runs, three hits and one walk in eight innings, losing for the first time in five starts. He dropped to 7-7 against the Rockies, but improved his ERA 20 points to 4.50 in 17 career starts.
"They beat us at every aspect of the game, and that's ultimately why we came up a little short," Lowe said. "They did a good job of manufacturing a run in the sixth inning and that was the ball game."
Colorado, which had lost three out of four and seven of 10, snapped a two-game losing streak.
The Braves have lost two straight and three of four.
"We hit three bullets in the eighth inning," said Braves manager Bobby Cox, whose team grounded into a season-high four double plays. "That was a game-changer. We didn't have any luck at all. We had one hit less than they did, and they got five runs. Figure that one out."
Dexter Fowler, who gave Colorado a 1-0 lead in the third with an RBI groundout, doubled leading off the sixth. He moved to third on a groundout and made it 2-1 on Todd Helton's RBI fielder's choice grounder.
Atlanta tied it at 1 in the sixth on a double-play grounder by Casey Kotchman.
The Rockies scored three runs in the ninth. Eric O'Flaherty, who relieved Lowe to start the inning, was charged with two runs after Troy Tulowitzki singled and Helton reached on shortstop Yunel Escobar's fielding error.
Peter Moylan, who relieved O'Flaherty, gave up consecutive RBI singles to Chris Iannetta and pinch-hitter Ryan Spilborghs. Iannetta scored from third on Clint Barmes' grounder, which third baseman Chipper Jones misplayed for an error.
Marquis, whom Atlanta drafted between the first and second rounds in 1996, came up through the Braves' farm system and made his debut in the majors four years later. He was traded to St. Louis the following winter after a 2003 season that included 19 relief appearances, two starts and a 0-0 record with a 5.53 ERA.
"He kept us off balance," Braves catcher Brian McCann said. "A lot of us were swinging at stuff out of the zone."
In his first four starts against the Braves, Marquis went 0-3 with a 14.04 ERA. After giving up six hits and two runs in 5 1/3 innings of a 10-2 win for the Chicago Cubs over the Braves last Aug. 13, Marquis is 2-0 with a 2.03 ERA in his last two starts against Atlanta.
Braves LHP Tom Glavine, on the DL all season with a sore shoulder, threw three simulated innings and hopes to make a rehab start Saturday. ... Atlanta CF Jordan Schafer made an over-the-shoulder catch a few feet from the wall to rob Tulowitzki of an extra-base hit in the third.