The loss dropped the D-backs out of third place and into fourth, a half-game behind San Diego.
It was an old nemesis that broke the game open for the Padres as Justin Upton smoked a two-run homer to right off Jeremy Hellickson in the fifth for a 4-2 lead. San Diego would tack on three more runs one inning later.
D-backs manager Chip Hale was kicking himself after the game for the Upton homer even though it was Hellickson that left the 3-2 fastball up on the outside corner of the plate.
"In that situation, I need to either walk him on four pitches or make it more clear to our guys that he's the guy that's not supposed to beat us," Hale said. "I take the blame for that. I think the pitch was supposed to be down and away and he got it up. Any time you don't walk him intentionally, as a manager, it's your fault. You can't expect your pitcher to be perfect."
Hellickson was trying to go away with the pitch, but he wanted to throw it down in the zone rather than up.
"I've just got to make a better pitch to that guy in that situation," Hellickson said. "If I walk, that's fine, the same situation a few innings before. But I don't think it was a terrible pitch. It just wasn't a good pitch right there."
The D-backs' offense, which teed off on Padres starter Andrew Cashner just six days ago for seven runs in four innings, did not have nearly the same success this time around.
The Arizona hitters collected three hits each in the second and third innings and three consecutive doubles in the third helped tie the game at 2, but after that, the bats were silent the rest of the way.
The lack of runs came on the heels of Friday night's series opener when they managed just two hits.
"I thought we battled and had the good inning with the doubles and put some runs on the board, but we just couldn't continue it," Hale said. "We're just getting stuck. We need to really start to get our offense going and help our pitchers out so they don't have to be perfect. I think they feel like they have to be perfect and we know we can score more runs than that."