The Padres also suffered another injury, as left fielder James Darnell exited in the sixth inning with a left shoulder subluxation (partial dislocation). He will undergo an MRI exam on Friday. The Padres currently have 10 players on the disabled list.
With the victory, the NL West-leading Dodgers (25-13) split the two-game series. The Padres won the opener, 4-2, Wednesday afternoon.
"We seemed to have more energy tonight," Dodgers manager Don Mattingly said. "Looking back on last night -- it was a perfect storm. Coming off a good homestand, we bused after the night game, played a day game. It seemed like we were a little flat. Tonight, there was different energy."
After winning his last two starts, Padres starter Edinson Volquez (2-3) struggled with his command. He allowed a season-high five runs (three earned) in five innings. He gave up seven hits, struck out six and walked three -- and two of those scored. His ERA is 3.04.
"He didn't quite have the command of all his pitches, hung in there, but still they got some big hits off him," Padres manager Bud Black said. "Didn't quite command the game like we've seen."
Volquez issued leadoff walks in both the first and second innings, and both runners went on to score. Dee Gordon walked in the first and scored on Bobby Abreu's triple, and the Dodgers added another run on Andre Ethier's single.
The Dodgers went up 3-0 in the second after A.J. Ellis drew a leadoff walk and eventually scored on Gordon's sacrifice fly.
"It's one thing we'll continue to stress with him," Black said about Volquez's walks. "He knows it. He and [pitching coach] Darren [Balsley] continue to work on his mechanics, his delivery to keep him a little more consistent in the strike zone."
Without Matt Kemp, the Dodgers outhit the Padres 12-5. Dodgers starter Aaron Harang (3-2) struck out six, walked none and allowed four hits in seven shutout innings.
John Baker's two doubles were the Padres' only extra-base hits. Alexi Amarista, called up from Triple-A Tucson earlier in the day, singled in the fifth for his first hit as a Padre. Amarista started at second base and fellow callup Everth Cabrera started at shortstop.
Chris Denorfia ended the shutout with his single in the ninth. Chase Headley scored after reaching on a two-base error.
"You've got to give credit to Aaron Harang," Baker said. "I don't know how many three-ball counts he even had at all tonight. He was throwing strikes and he was making us swing the bat."
The Dodgers scored two runs in the first, fifth and seventh innings. Their two runs in the fifth were unearned, and they added an unearned run in the ninth. Abreu doubled and scored on center fielder Cameron Maybin's two-base fielding error in the fifth. James Loney drove in another run with a double.
The Dodgers scored another unearned run on the ninth, after reliever Miles Mikolas committed a two-base throwing error.
The Padres have committed 39 errors and allowed 25 unearned runs this season.
In their first games with the Padres this season, Cabrera went 0-for-3 and Amarista went 1-for-3. Second baseman Orlando Hudson was released Thursday and shortstop Jason Bartlett went on the DL.
"They had some good swings," Black said.