SAN DIEGO -- With his chance for the decision wiped away by an error, Brandon Webb got the next-best thing thanks to scrappy Eric Byrnes.
"Webby threw such a great game that we wanted to at least come away with a win for the team, because an effort like that, you don't want it to go to waste," Byrnes said.
San Diego's bullpen gave up a run for the first time in 14 innings over two games when Byrnes singled in Scott Hairston. Orlando Hudson followed with a two-run double.
The Padres' bullpen threw nine scoreless innings in a 4-3, 14-inning win at the Chicago Cubs on Tuesday, then had four scoreless innings before the Diamondbacks finally broke through.
Hairston started the winning rally with a two-out double to left-center off Mike Thompson (0-1). Stephen Drew was intentionally walked to bring up Byrnes, who singled to right.
"You're not human and probably not playing baseball at this level if you're not going to take that personally," Byrnes said. "I'm sure they have their reasons, but when I come in that situation, when they walk the guy in front of you, you're going to have a little extra focus in those at-bats. Obviously you're going to want to make him pay for that."
Tony Pena (1-1) pitched a perfect 11th. Jose Valverde pitched the 12th for his seventh save in eight chances.
Padres starter David Wells was ejected in the 12th for saying something to first base umpire Doug Eddings from the dugout after Arizona's Alberto Callaspo reached on an error by Thompson. Eddings ruled that Thompson didn't have his foot on the bag. Callaspo was erased on a 5-6-4 double play on Robby Hammock's bunt.
Wells said replays showed Thompson got to the bag in time. The big left-hander said he was frustrated because Eddings didn't give him the call on a check swing by Conor Jackson in the seventh with two strikes. Jackson eventually walked with the bases loaded.
"You see a swing like that, you get riled up," Wells said. "I said, 'You didn't miss one, you missed two.' Things started to heat up and he was chirping and chirping. That's when he tossed me out."
Wells said Eddings rubbed his belly and said, "You're fat."
"I think that's stepping over the line," Wells said.
Eddings denied that, saying, "That's false. I would never."
San Diego's Brian Giles went 4-for-6, all singles.
Webb and Wells were locked in a 1-1 duel before Wells allowed the first four batters to reach in the seventh, with the go-ahead run scoring on a walk.
The Padres came back and tied it at 2 with an unearned run in the eighth, costing Webb a shot at the decision.
Giles reached leading off the inning when his routine fly ball to center hit off the front of Chris Young's glove for an error. Adrian Gonzalez drew a one-out walk before Khalil Greene, who struck out in his first three at-bats, singled in Giles.
Webb's previous strikeout high was 11, accomplished three times. He allowed two runs, one earned, and seven hits in eight innings, with one walk.
"Usually I don't strike out many and that's not really what I'm trying to do," Webb said. "Tonight my off-speed stuff was pretty good. I was getting ahead of hitters and working my off-speed late and it was getting the punchies after that. Usually I'm trying to get the quick outs off ground balls. It worked out a little bit different."
Wells gave up two runs and three hits in seven innings while striking out four and walking one.
Webb, 27, and Wells, 43, pitched brilliantly for six innings.
Stephen Drew opened the game with a double to short right-center that fell in front of Mike Cameron before Wells retired the next 18 batters. Wells gave up Arizona's only run in the process, as Drew advanced on Byrnes' fly to left and scored on Hudson's groundout.
Webb, who beat out Padres closer Trevor Hoffman for the 2006 NL Cy Young Award, struck out nine of 11 batters early in the game, including six in a row.
Wells got into trouble opening the seventh when he allowed singles to Byrnes and Hudson before hitting Carlos Quentin on the foot with a pitch. Jackson fell behind 0-2 before drawing four straight balls -- including one on a check swing -- to force in Byrnes with the go-ahead run.
Wells limited the damage, though, by getting Young to fly out and inducing grounders by Callaspo and Chris Snyder. Wells pounced on Callaspo's dribbler to force Hudson at the plate.
Webb also allowed a run in the first inning. Marcus Giles hit a leadoff single to center, advanced to third on brother Brian's single to left and scored on Cameron's grounder.
This two-game series concludes Thursday afternoon. ... The teams will meet again in a three-game series in Phoenix starting next Tuesday night, and the Padres might be facing Randy Johnson that night. The Big Unit, returning from offseason back surgery, is scheduled to make one more start for Triple-A Tucson before joining the Diamondbacks' rotation.