The win was the second in a row for the D-backs and it came in the first game of a nine-game, three-city trip.
"This guy has been doing it for a long time and tonight, he got back to the form that made him that," said Padres manager Bud Black of Arroyo.
Arroyo (2-2) was signed to a two-year free-agent deal just after camp opened and a bulging disc in his back caused him to miss a few starts. That put him behind the other starters and when the season opened he was not quite sharp.
Then just as he was rounding into shape he came down with a virus that left him feeling under the weather during his last start.
Arroyo was feeling better this week and it showed as he kept the Padres off balance, limiting them to just three singles.
"They ran a lot of lefties at me as usual," Arroyo said of the Padres, who started five lefties and a switch-hitter against him. "I got a chance to take advantage of a bit of their aggressiveness on the outer half, hitting a lot of ground balls to second base. I had a little more zip tonight. I'm starting to feel a little better. It makes a difference for me when I can get the ball up to 88-89 mph once in a while. It makes them respect some of my other stuff a bit more."
The D-backs gave him some runs to work with in the third inning when Aaron Hill delivered a two-out, two-run single off a hanging slider.
"He's got such a good fastball you have to be ready for it, obviously," Hill said. "He was keeping it down all night and luckily he threw me a slider that was a little bit up. I put a good swing on it and luckily it worked out."
That was all that Padres starter Andrew Cashner (2-4) would allow, but it was enough to hang him with a loss.
Arroyo committed an error on Padres leadoff hitter Everth Cabrera's first-inning grounder, but that was the only baserunner he allowed until Yonder Alonso's one-out single in the fifth.
Brad Ziegler held the Padres at bay in the eighth and closer Addison Reed pitched the ninth to earn his seventh save.
"It was a smooth one from front to back," Arroyo said. "It was definitely the way you want to start off a road trip."
Starting pitching has been an issue for the D-backs all year, with the starters struggling to pitch deep into games. If Arroyo, who has thrown at least 199 innings in each of the last nine seasons, is able to start piling up the innings, it will be a huge lift.
That was something he didn't feel like he was able to do after being set back during Spring Training.
"I've always been kind of a thin guy and I'm getting up in age," the 37-year-old said. "Missing three weeks of Spring Training was tough on me. People don't realize what it takes out of a guy like me to not be able to go in the weight room and lift and be able to stay strong.
"The body starts atrophying pretty quick. For some of the bigger, stronger, younger guys, they can go out there and feel like their arm is really fresh. But for me, I need a lot of work in order to stay kind of strong. As the season gets going, you kind of get into a routine and I really didn't have that in spring. I'm starting to feel pretty good right now."
The win was the 300th of Kirk Gibson's managerial career, though he is less focused on that given his team's sluggish start.