Jennings, who was 0-1 with a 13.50 ERA over his previous three outings, allowed six hits in six innings. Justin Speier, Jay Powell and Jose Jimenez worked an inning apiece to preserve the shutout.
Johnson recorded a shutout against the Mets in his major league debut on Aug. 23.
San Diego's Rickey Henderson, who needs two hits to become the 25th member of the 3,000-hit club, was hitless in four at bats.
Larry Walker and Todd Helton provided Jennings with all the run support he needed with back-to-back home runs in the top of the sixth inning.
They hit consecutive pitches from San Diego starter Kevin Jarvis to give the Rockies a 4-0 lead. Walker's homer was his 38th of the season and Helton's was his 49th, which tied Walker's franchise record set in 1997.
Jarvis (12-11) allowed four runs and six hits in seven innings. The two homers increased his total to 37, tying the club record set by Bobby Jones on Wednesday.
The Padres (78-82) clinched their third consecutive losing season.