The Padres improved to 28-4 this season when scoring four or more runs, the second-best mark in baseball behind Washington, which is 39-3 when scoring at least four times.
Kennedy got all the support he needed after the fifth.
With the score tied 1-1 in the sixth, Tommy Medica hit a one-out double and Rene Rivera followed with a double to left. One out later, Cameron Maybin sent a drive to the warning track in left center that seemed to get caught in swirling winds and dropped just beyond the reach of Dickerson's glove as the Padres took a 3-1 lead.
"I felt like I got there pretty good and then I saw Stubbs pretty close," Dickerson said. "Nobody called it so I called it but I felt he was still running, too. It was a difficult play."
San Diego added three runs in the seventh. Kennedy drew a leadoff walk and Chris Denorfia singled to chase Matzek (1-3). Headley greeted Matt Belisle with a triple off the right-field wall, scoring Kennedy and Denorfia. Carlos Quentin's sacrifice fly put the Padres in front by five runs.
Matzek was charged with five runs and eight hits in six-plus innings. He walked four and struck out four.
"I started falling behind guys. I was picking corners and trying to be fine," Matzek said. "First-pitch strikes are the most important thing. You get hitters in hitters' counts and they're going to hit the ball."
NOTES: Padres RHP Tyson Ross is slated to start Tuesday's Game 2 against LHP Franklin Morales and the Rockies. ... Stubbs is batting .333 (6 for 18) with two home runs midway through the Rockies' 10-game homestand. ... Rockies batters struck out 13 times in all.