Right-hander Tim Stauffer tossed six innings in his second start for the Padres this season. He allowed one run on three hits with two walks and four strikeouts.
Padres manager Bud Black said he didn't think Stauffer appeared as "crisp" as he was July 11 against the Giants in his first appearance this season.
In that start, Stauffer allowed two runs on four hits, striking out seven and walking one in seven innings of work. Black said he saw more of a gritty effort from Stauffer on Monday, characterized by his determination to get through.
"Stauffer did a nice job," Black said. "He made his pitches, and I liked the use of the changeup."
Stauffer, who missed the 2008 season because of right shoulder surgery, said he agreed with Black's assessment that he lacked crispness.
"It was kind of one of those where you're feeling a bit fatigued, battling in each inning," he said. "I was giving us a chance to win, which is what you ask for from a starting pitcher."
The Marlins got their only run off Stauffer on Hanley Ramirez' two-out solo shot to left field in the first inning.
"He's a great hitter and he made me pay for it," Stauffer said.
The Padres briefly held a 2-1 lead after the home runs in the sixth inning. Gonzalez's shot was his first since June 23, spanning 83 at-bats. He is now tied for second place in the Major Leagues with Raul Ibanez of the Phillies.
"I know my home runs will come in streaks," Gonzalez said.
The excitement from the homers was short-lived, as the Marlins capitalized on the Padres' bullpen woes in the seventh.
Reliever Greg Burke allowed three consecutive singles to start the inning. The Marlins tied the game at 2 when John Baker grounded out to score Jeremy Hermida.
With the bases loaded, Padres reliever Luke Gregerson replaced Burke and fanned Chris Coghlan for the second out of the inning.
But Gregerson then walked Emilio Bonifacio, driving in the go-ahead run for the Marlins in the seventh. Gregerson stuck out Ramirez to end the inning and retired three batters in the eighth.
"He could have caved in after the walk, but he didn't," Black said.
Burke (2-2) absorbed the loss for the Padres, allowing two runs on three hits in one-third of an inning. He had one walk and no strikeouts.
The Padres' best chance to drive in the tying run came when Everth Cabrera walked as the leadoff hitter in the eighth. Cabrera advanced to second on Tony Gwynn's sacrifice bunt and reached third on a groundout by Gonzalez, but Kouzmanoff grounded out to end the inning.
Oscar Salazar, whom the Padres acquired Sunday from the Orioles in exchange for pitcher Cla Meredith, made a pinch-hitting appearance with one out in the ninth inning. Salazar showed some impressive speed when he reached base on a throwing error by third baseman Bonifacio.
"I was prepared to go in sometime after the sixth inning, from what the bench coach told me," Salazar said. "I just tried to put the ball into play and make something happen."
Marlins closer Leo Nunez retired Luis Rodriguez and pinch-hitter Kyle Blanks to end the Padres' comeback hopes.