Chase Headley doubled in three runs, and the Padres roughed up Bauer 9-5 in his home debut Tuesday, winning their fourth straight and sending the Diamondbacks to their fourth loss in a row.
Hard-throwing Padres starter Andrew Cashner left the game after two innings with a strained muscle in his right side. Leading 2-0 at the time, the Padres scored five in the fourth to break open the game. The injury was diagnosed as a strained lat muscle.
Yonder Alonso hit a two-run homer for San Diego.
Bauer (0-1), the third pick overall in last year's draft, allowed six earned runs and six hits in 3 1/3 innings.
"There were instances throughout the game where I threw the wrong pitch," Bauer said. "I wasn't as convicted on stuff as I should have been. I think it is a comfort thing."
Still, he said "there's no reason to panic."
"It is a bad outing," Bauer said. "It gets magnified because it is a big league outing instead of a minor league outing but I am not worried about it."
Bauer walked four and struck out six.
"As the game went on, guys kind of figured out what he was doing," Headley said. "He's unorthodox to say the least, as far as his mechanics, a lot of stuff flying at you. I think the biggest thing that got him was just kind of loss of control. He put himself in some tough positions."
Arizona's Paul Goldschmidt matched his career best with four hits, all singles, including one for an RBI with two outs in the ninth.
Ohlendorf was responsible for three runs in 2 1/3 innings after leaving the game with the bases loaded and one out in the fifth. His replacement, Nick Vincent, struck out Justin Upton, but Kubel homered into the right-field seats to slice the lead in half at 8-4. It was Kubel's first slam since July 25, 2009, for Minnesota at Baltimore.
Cashner, making his third start of the season and fourth of his career, hit 101 mph on the Chase Field radar gun. He left after taking the mound but not throwing a pitch in the third inning. He threw just 28 pitches.
"He felt it and he did the right thing," San Diego Padres manager Bud Black said. "He said, 'Buddy, I thought I could keep going, I could keep throwing, but I thought, you know, based on last year, I wanted to let you know.'"
Cashner missed five months with a strained right rotator cuff with the Chicago Cubs last season.
His injury dampened another strong outing by the Padres.
"Overall it's been a factor of better team defense, better pitching and more timely hitting," Black said, "and a little less shuffling of the deck so to speak, getting a little better feeling of our players."
Bauer, the quirky former UCLA star with an unorthodox 90-minute warm-up that features soaring tosses from near the right-field line to the left-field line, struck out the first three batters he faced.
But Bauer fell behind in the second after Yasmani Grandal's one-out single and Alonso's first-pitch shot over the right-field fence. He contributed to his own demise with an error in the fourth.
One-out singles by Cameron Maybin and Everth Cabrera put runners on first and third, then Ohlendorf put down a suicide squeeze bunt that went right to Bauer. The youngster, eying a throw home, bobbled the ball and everyone was safe. Will Venable singled to load the bases, and an RBI single by Alexi Amarista made it 4-0. Headley cleared the bases with a double to deep center, and the blowout was on at 7-0.
Bauer made his major league debut Thursday at Atlanta, allowing two runs on five hits in four innings, getting no decision in a 3-2 Diamondbacks victory.
Kubel's throwing error in the fifth brought in the Padres' eighth run, then Guzman's pinch-hit home run in the eighth made it 9-4.
The Padres, winners of the first two games of the series, go for their second three-game sweep of the season Wednesday night. Arizona had won 10 of 11 at home before opening this seven-game homestand with two losses to the NL West's last-place team.
2B Aaron Hill doubled and singled to extend his home hitting streak to 18 games, matching the fourth-longest in Arizona history. ... The Fourth of July night contest, featuring postgame fireworks, is the Diamondbacks' first sellout since the season opener. ... San Diego has won three of its past four series and split the other one, although the competition has been Seattle, Houston, Colorado and Arizona, none of which has a winning record. ... Arizona LHP Joe Saunders threw 51 pitches Tuesday. He's been on the 15-day DL since June 23 with a strained left shoulder. ... The Padres send Jason Marquis (1-4, 3.06 ERA) to the mound Wednesday night, while Arizona looks to stem its skid with Ian Kennedy (6-7, 4.20). ... The Diamondbacks set a franchise record for a single season by homering in 14 straight games. ... Kubel, signed in the offseason as a free agent, has 55 RBIs.