Alex White (1-1) worked five innings, giving up four runs on five hits while striking out six and walking three to earn his first National League win.
"Hopefully there will be many more to come behind it," said White, who came over from Cleveland in the Ubaldo Jimenez trade.
Rafael Betancourt worked a perfect ninth to notch his sixth save of the year.
Cory Luebke (5-8) lasted 4 1/3 innings in defeat, giving up five runs on eight hits while fanning five and walking one.
"I just wasn't consistent," said Luebke. "I couldn't locate my fastball and that's always been the key to my success. I just didn't do it tonight."
In the pivotal fifth frame, the eventual winning run came when Fowler singled to begin the inning, stole second and came around to score on a single by Tulowitzki to make it 5-2.
San Diego fought back to make it a one-run game in the home half of the inning when pinch-hitter Aaron Cunningham walked and Venable ripped a double to put runners on second and third. After a Jason Bartlett strikeout, Guzman brought in both runners with a double to right to make it 5-4.
The Padres had a shot to take the lead in the home eighth when Kyle Blanks singled and Jeremy Hermida walked to put two runners on with two outs against Rockies reliever Rex Brothers. San Diego was unable to capitalize however, as Brothers fanned Alberto Gonzalez to end the inning.
Earlier, Colorado jumped out in front in its first at-bat when Fowler ripped a double to begin the game and was chased home on a single to left by Carlos Gonzalez.
The lead didn't last long, as the Padres got the run back plus one in the home half of the inning when Venable crushed a fastball from White deep into the seats beyond the center field wall to tie the game. Nick Hundley singled home Guzman to give San Diego a 2-1 lead.
The Rockies plated three runs in the fourth to take the lead for good at 4-2. Tulowitzki led off the inning by clubbing a double into the right-center field gap and came around to score on a single by Helton. Kevin Kouzmanoff singled to put runners on first and second and Ryan Spilborghs then doubled home Helton to make it 3-2. Colorado then added its fourth run on a sacrifice fly by Chris Iannetta.
Saturday continued a six-game homestand for the Padres...Colorado leads the season series with the Padres by a 9-5 count...The Rockies are 26-32 against the National League West, while the Padres are 18-34 against intra-division competition...By dropping the first two games of the series, San Diego has now lost six of its last seven series against Colorado.