Cook gave up the first run of the game in the second inning after Will Venable hit a triple to right and scored on a wild pitch.
But then the Rockies' bats came alive.
In the third, Clint Barmes led off with a single and Willy Taveras hit an RBI double to right to plate the Rockies' first run.
Three batters later, Garrett Atkins hit a two-run home run to left to give the Rockies a 4-1 lead.
"Just trying to find a way to get the ball in the air and score a run," Atkins said. "He left it out over the plate a little bit and I was able to get all three runs in."
Padres starter Dirk Hayhurst would only last till the fourth inning after giving up four runs on five hits with four strikeouts and four walks.
The Padres would make the score 4-2 in the bottom of the third on a RBI single by Adrian Gonzalez. It would be the last run Cook would give up, as he went six innings, allowing two runs on five hits with three strikeouts and two walks on 95 pitches.
"I thought there was a lot of improvement in some areas, but he had to grind through every inning just about," Rockies manager Clint Hurdle said. "He said he felt really good. I think it was a real nice step back in the right direction. He pitched through some traffic but all in all it was his best outing in a while."
It was the first time since July 25 that Cook had given up five hits or less.
The Padres would make the score 4-3 in the bottom of the seventh on a home run to left by Nick Hundley, as they looked poised for a late comeback as they did in their previous game against the D-backs. But that would be the closest the Padres would get.
The Rockies tacked on another three runs in the eighth on a Seth Smith pinch-hit two-run double to left and Chris Iannetta scoring from third on a wild pitch by Padres' reliever Brian Falkenborg.
"It's always a struggle to score a lot of runs in this park, especially at night, because the ball doesn't travel that well," said Matt Holliday. "It's a big yard and they have good pitchers, but we've had a few games here where we've scored some runs."
In the final frame, after Holliday extended his hit streak to 10 games with a single to center, Atkins followed two batters later and put another one in the seats, this time to center field.
"This is a ballpark that you usually don't throw a couple out there," Hurdle said. "The first one was hit deep a little bit earlier in the day, so that doesn't catch your eye as much, but that last one will get your attention."
Atkins, hitting .375 in San Diego this season, seems to be able to find a comfort zone in a ballpark where most hitters have problems producing power numbers.
"The last time up, just going up there, trying to be aggressive," Atkins said. "I remember facing [Falkenborg] when he was with the Dodgers and just looking for a fastball over the plate. And I had one of the better swings I've had all year off of it."
As the Rockies racked up their nine runs on 10 hits in a supposed pitchers' park, Atkins can't seem to figure out why his teammates, and particularly himself, are able to produce some runs.
"I don't know what it is," Atkins said. "It's San Diego. It's always nice weather. Just a nice place to play, nice ballpark. I just seem to have had some success here."