Stults (2-2) scattered five hits over 5 1/3 scoreless innings, walking two and striking out five. Stults, making his first start since being promoted from the bullpen, threw 54 of his 79 pitches for strikes.
Brad Brach, Dale Thayer and Luke Gregerson combined for 2 2/3 hitless innings and Huston Street set the Cubs down 1-2-3 in the ninth for his 19th save as San Diego won the opener of a three-game series.
Yonder Alonso and Everth Cabrera each delivered an RBI single in the fourth inning to provide the Padres' offense.
Chicago's Travis Wood (4-8) took the loss, allowing two runs on five hits in a six-inning stint. The Cubs left-hander walked three and fanned three.