Stults (8-17), tied with Philadelphia right-hander A.J. Burnett for the major league lead in losses, scattered seven hits and a walk over 6 1-3 innings in beating the Rockies for the first time this season after two defeats.
Kevin Quackenbush worked the ninth for his sixth save, ending Colorado's season-high, six-game winning streak.
San Diego went ahead in the first inning when Rene Rivera's double scored Jedd Gyorko, who walked. It was Rivera's fifth RBI and third double in four games.
Rockies starter Tyler Matzek (6-11) struck out eight in six innings. He allowed one run, four hits and three walks.
To open the eighth, Padres left fielder Tommy Medica misplayed Justin Morneau's fly ball into a double and Dale Thayer relieved Frank Garces. Thayer got Michael Cuddyer and Corey Dickerson to pop up and retired Michael McKenry on a fly to center.
After DJ LeMahieu's one-out single in the seventh chased Stults, he was replaced by Nick Vincent. Pinch-hitter Drew Stubbs struck out and, after Charlie Blackmon singled, Vincent retired Josh Rutledge on a fly to right.
The Padres could have extended their 1-0 lead in the sixth when they loaded the bases with one out on Rivera's second hit and walks to Gyorko and Yasmani Grandal. Matzek, however, struck out Medica and Rymer Liriano.
The Rockies had an opportunity in the fifth inning when Blackmon walked with two outs to load the bases, following singles by Rafael Ynoa and LeMahieu. Stults struck out Rutledge on one his quickest fastballs, at 90 mph, to retire the side.
Stults wiggled out of trouble in the second after giving up one-out singles to Dickerson and McKenry. Ynoa popped up and LeMahieu struck out.
The Padres are 32-19 in one-run games, the best record in the majors.
Padres: RHP Tyson Ross, bothered by a sore right forearm, won't pitch again this year. His last start came on Sept. 13 at Arizona when he gave up six runs (four earned) and five hits in three innings.
Rockies LHP Jorge De La Rosa (14-11, 4.61 ERA) will tie a career high Tuesday when he makes his 32nd start of the season, his second straight year with at least 30. He'll face Padres LHP Robbie Erlin (4-4, 4.53), who is looking for his second consecutive win as he makes his second start since May 17 at Colorado.