They didn't, thanks again to a handful of reserves who have filled in admirably for injured starters.
The Padres led 5-0 after five innings, let the Diamondbacks tie it in the top of the sixth and then scored five runs off Arizona's bullpen in the bottom of the inning. Sweeney, filling in for injured first baseman Phil Nevin, and Jackson, playing for second baseman Mark Loretta, each had a hit and scored during the sixth-inning rally.
"That's tough when you have the lead and they tie it," manager Bruce Bochy said. "They came back, but we came right back and put a five-spot on them. That's what's important. Nobody got down. It shows how resilient the club can be. That's huge."
Trevor Hoffman came in with runners on first and second and one out in the ninth, threw a wild pitch and walked Jose Cruz Jr. to load the bases. Royce Clayton hit a sacrifice fly before Hoffman struck out Kelly Stinnett for his 26th save in 28 chances and the 419th of his career.
The win put the NL West-leading Padres 5½ games ahead of Arizona, their closest pursuer in baseball's worst division. The Diamondbacks won the series opener 6-0 on Thursday night.
Making a rare pinch-hitting appearance, Arizona's Troy Glaus
drove a three-run homer into the second deck in left field that tied the game at 5 with two outs in the sixth. It was the 20th homer for Glaus, who didn't start because he has been bothered by a strained tendon in his left knee.
The Padres blew it open on five hits and a walk in their half.
Greg Aquino (0-1) allowed consecutive singles to Sweeney and Ramon Hernandez before getting the first out. Lance Cormier came on and allowed Khalil Greene's RBI single that gave the Padres a 6-5 lead. Dave Roberts drove in a run on a groundout before Jackson had the inning's big hit, a two-run single to right.
"That's what it takes is a team effort, especially now, when we're a little dinged up," Giles said. "We've got guys going out there that aren't used to playing every day who are doing an excellent job for us."
Arizona manager Bob Melvin said that was the first time Cormier "went out there and couldn't stop the bleeding. We felt like we had a good chance to get out of the inning."
San Diego's Woody Williams took a four-hit shutout into the sixth before the Diamondbacks rallied.
Shawn Green hit a solo homer to right with one out, his 15th. Williams retired Chad Tracy on a fly to left but allowed Cruz's single and walked Clayton. Chris Hammond came on and gave up pinch-hitter Tony Clark's RBI single.
"I have never really done it," Glaus said of pinch-hitting. "I didn't know what to do. I was trying to get at least one good swing in and it worked out pretty good."
San Diego took a 5-0 lead on Klesko's two-run homer in the first, Sweeney's solo shot in the fourth -- both with two outs -- and two unearned runs in the fifth.
Sweeney's homer, his seventh, helped him atone for getting thrown out trying to go all the way to third on Webb's errant pickoff throw following his two-out single.
Jackson had an RBI single and Giles a sacrifice fly in the fifth. Both runs were unearned because of a throwing error on catcher Chris Snyder. Cruz hit a sacrifice fly in the seventh.
Webb pitched five innings, allowing five runs -- three earned -- and eight hits while striking out three and walking one. Williams went 5 2/3 innings, allowing three runs and six hits. He walked three and struck out two.
Glaus stayed in the game at third base after his pinch-homer. Cintron started at third. ... Padres right-hander Adam Eaton, on the DL since June 16 with a strained right middle finger, said his goal is to be back by Aug. 1. Eaton played catch on Friday and is scheduled to throw bullpen sessions on Saturday and Tuesday, a simulated game next Friday and a rehab start on July 26, most likely for Class-A Lake Elsinore. ... Padres second baseman Mark Loretta reported to Triple-A Portland on Friday for a rehab assignment and is due to be activated from the DL on Tuesday in New York. First baseman Phil Nevin is scheduled to join Loretta with Portland on Saturday and he might be activated Tuesday as well.