"Right now you've got to take whatever they give you," catcher Miguel Montero said.
Thanks to the win, the D-backs have a chance to capture the series and break even on their six-game road trip, if they can find a way to win Sunday.
With the score tied at 2, the D-backs had runners on the corners with one out against reliever Joe Thatcher.
Gerardo Parra, the runner on third, faked like he was going to steal home and Thatcher flinched just a bit for the balk that allowed Parra to score the go-ahead run.
"To be honest, Parra kind of fooled me on that," Montero said. "I was on the bench and I was like 'Whoa, what are you doing man?' That was a big run for us right there."
Thatcher disputed third-base umpire Brian Gorman's call.
"I feel like it was a pretty ridiculous call," Thatcher said. "I didn't do anything. Once Parra and the third-base coach started yelling, I think he [Gorman] figured he had to make a call."
Parra got the start in right field in place of Justin Upton and made the most of his opportunity.
In addition to helping to cause the balk, Parra coaxed the bases-loaded walk in the eighth that gave the D-backs an insurance run.
Parra also contributed on defense, throwing a strike to third to nail Yonder Alonso, who was trying to tag up on Carlos Quentin's fly out.
"Parra had a heck of a game," D-backs manager Kirk Gibson said. "It was very clutch play by Parra today. He did a great job, a big game for him."
In the second Parra grabbed Evereth Cabrera's double off the wall and threw a strike to second baseman Aaron Hill, who in turn made a good relay to third to cut Cabrera down trying to stretch it into a triple.
"He made two strong throws and had one good relay," Padres manager Bud Black said of Parra. "I thought with both plays they had to execute and they did."
In his second outing since coming off the disabled list, Hudson (2-1) allowed two runs on five hits over eight innings.
"Huddy of old," was how Gibson described him.
Hudson, who missed six weeks with an impingement in his shoulder, fanned five and walked just one.
"He looked good," Montero said. "He was Huddy. He kept the ball down and made good quality pitches when he needed it and he got quick outs."
Hudson, who won the National League Silver Slugger Award last year, helped himself with his bat in the fourth.
After the D-backs loaded the bases with no outs, Padres starter Edison Volquez got Hill to pop out.
Hudson, though, followed with a sacrifice fly to right to score Montero and give Arizona a 1-0 lead.
The lead did not last long as Will Venable led off the bottom half of the inning with a bunt single, stole second and scored when Cameron Maybin followed with a single to right.
Maybin advanced to second when Parra threw home trying to nail Venable and he scored when Alonso singled to center to give San Diego a 2-1 lead.
Paul Goldschmidt hit a solo homer in the fifth to tie the game.
Cabrera led off the eighth with a walk and Gibson went out to the mound to talk to Hudson, who told his manager that he wanted to stay in the game.
"I didn't want to take the game away from him so I stayed with him," Gibson said.
Said Hudson, "He asked me how I felt and I felt fine and he said, 'OK, get a double play and let's get out of this thing.'"
Hudson didn't get a double play, but he did manage to get out of the inning and closer J.J. Putz set the Padres down in the ninth to seal the win.