Tuesday's results forced the Dodgers to keep on ice the champagne they'd lugged with them from Pittsburgh, where they lost three of four to the Pirates, the NL's second-worst team.
Heath Bell, who turned 32 on Tuesday, pitched a perfect ninth for his NL-best 41st save in 47 chances, striking out Manny Ramirez, Matt Kemp and James Loney.
With his Hall of Fame father doing color commentary on the local cable broadcast, Gwynn hit a drive down the right-field line with two outs in the third inning for a 1-0 lead. It was his second homer of the season.
The Dodgers tied it in the sixth when Orlando Hudson hit a leadoff triple into the gap in right-center field and scored when rookie shortstop Everth Cabrera booted Andre Ethier's grounder.
That brought up Ramirez, and Padres manager Bud Black pulled rookie left-hander Cesar Ramos, who was making his first big league start, in favor of rookie righty Ryan Webb (2-0), who got the slugger to hit into a double play. Kemp grounded out to end the inning.
Ramirez missed Monday's 11-1 loss at Pittsburgh with tightness in his left hamstring. He went 0 for 4 with two strikeouts on Tuesday night.
Chad Billingsley walked the bases loaded with two outs in the sixth before Kouzmanoff singled up the middle to bring in David
Eckstein with the go-ahead run. Adrian Gonzalez was thrown out trying to score from second.
Billingsley (12-11) lost for the fifth time in his last seven starts. He hasn't won since Aug. 18 against St. Louis. He allowed two runs and two hits, struck out five and walked five in six innings.
Billingsley has yielded a home run in seven of his last eight starts, and Gwynn's shot was the 17th allowed by the right-hander this season, extending his career high.
San Diego added a run in the seventh on Hong-Chih Kuo's wild pitch.
The first two Dodgers batters of the game reached and neither scored. Rafael Furcal singled to left to extend his hitting streak to 12 and Hudson walked. Ethier hit into a 4-3-6-5 double play, where the Padres had Hudson in a pickle between first and second, then let him advance as they caught Furcal at third after he took a step too many toward home, then tried to get back to the base.
The Dodgers stranded two runners in the sixth.
Ramos, making his fourth big league appearance, allowed one run and four hits in five innings.
NOTES: Dodgers manager Joe Torre said left-hander Randy Wolf will start Friday night at home against the Rockies, but beyond that, he didn't name starters for the rest of the weekend series. However, he said LHP Clayton Kershaw, who missed three weeks with a right shoulder injury, needs to throw about 90 pitches this weekend. ... Torre will have to cut his six-man rotation to four for the playoffs. ... Los Angeles' Casey Blake and Ronnie Belliard both continued to sit out with injuries. ... Gonzalez walked three times to extend his career high to 113 and take over the NL lead over Albert Pujols and Adam Dunn, each with 112.