"It's unbelievable," catcher Miguel Montero said. "Last place and get swept by that team. They're hitting at the right time, and they made the right pitches at the right time."
The D-backs will head home to Phoenix empty-handed after sending their big three starting pitchers -- Dan Haren, Brandon Webb and Johnson -- to the hill. Between the three of them, they had 43 combined wins entering the series, just five fewer than the Padres had as a team.
"That's why you've got to play the game," Johnson said. "We kind of just have to go back to the drawing board."
Johnson did it on the mound and with his bat Wednesday, as he had two hits and an RBI -- the first time since Sept. 14, 2003, that he had two hits in a game -- but his quest to join the 300-win club in 2008 is wearing thin.
"He's pitched great," Montero said. "He's been pitching and been battling out there. ... Unfortunately, he didn't get the win, but he threw an outstanding game. He has nothing to complain about."
The D-backs actually gave the Big Unit three runs of support, four if you count his own sixth-inning RBI single. But after allowing a couple hits and a two-run homer to Padres catcher Nick Hundley, Johnson's lead was down to just one run, which hasn't been enough for the D-backs' bullpen recently.
"It seems like all our games he has to pitch, we're not getting too many hits early on," D-backs manager Bob Melvin said. "He's got to be perfect, which he was. Then we get a little bit of a lead for the first time in a while in his games, and then pretty quickly it was 4-3."
Hundley, who grew up a huge Johnson fan just outside of Seattle, hit a 374-foot shot to left field to make the score 4-3 in the bottom of the seventh.
"I'm not going to say it was a bad pitch," Johnson said. "It was down, and he hit a home run. I was still winning the ballgame. I got through the inning, and we were still winning, so that's all that matters."
Qualls came in to relieve Johnson in the eighth and allowed a leadoff single to pinch-hitter Brian Giles on the first pitch. After shortstop Luis Rodriguez sacrificed Giles to second, Kevin Kouzmanoff struck out. Left fielder Chase Headley then hit a tying single to right field. After stealing second base, D-backs killer Jody Gerut slammed a go-ahead single.
"The first matchup was good for him," Melvin said of Qualls. "He's our best guy off Giles. ... We just had to make a better pitch to Gerut there. I think it was a slider that just kind of stayed [in the] middle. So he's our freshest arm at the time; he just got some balls up."
Gerut finished the season series hitting .432 (16-for-37) against the D-backs in 12 games, including a walk-off homer in Monday night's 4-2 win.
Qualls entered the game with 21 holds, fourth in the National League. This time, he was credited with a blown save.
After San Diego's comeback in the eighth, all-time saves leader Trevor Hoffman came in and struck out the side.
The Padres benched their two best offensive threats -- Adrian Gonzalez and Giles -- but were still able to come back to defeat the first-place D-backs.
"We've been through several periods like this this year, where we've had to respond, and we have," Melvin said. "Our division hasn't played great; our record doesn't look great, but we've responded. We've had a lot of games where we've been heartbroken this year.
"I didn't foresee getting swept here with those three pitchers, but we have to deal with it. We've got to move on."