Steve Cishek (4-0) got the victory in relief for the Marlins with three scoreless innings.
Trailing, 8-7, the Padres tied the score in the ninth inning when Cameron Maybin had an RBI double to score Jesus Guzman, who doubled earlier in the inning against former Padres closer Heath Bell.
It was the fourth blown save of the season for Bell, who was a three-time All-Star with the Padres from 2009-11.
I've got to keep fighting," Bell said. "It's just one of those things where I'm having bad luck right now. I think I made some pitches when I needed to. What can you do? I'm just going to keep my head up and keep going."
The game was filled with some crazy twists, as the Marlins jumped out to a 5-0 lead in the first inning and then trailed, 6-5, after the Padres scored six runs in the third.
"It was a pretty long game, but we were battling," said Padres first baseman Yonder Alonso, who had a career-high four hits in a game that lasted four hours and 45 minutes. "You could tell early that it was going to be a good night with the bats."
The Padres had 15 hits but left 16 on base.
Three of the Padres' six runs in the third came on pitcher Anthony Bass' first big league hit, a triple to right field. Bass had a second hit later in the game.
"I could hit back in high school, but that was high school," said Bass, who said he had one hit in six at-bats in the Minor Leagues.
Bass allowed six runs on six hits with three walks and seven strikeouts over six innings. He allowed one run on two hits over his final five innings. He was in line for the victory before the Marlins rallied in the seventh with two runs off reliever Luke Gregerson.
"That's really a tribute to Anthony, the way he hung in there," Padres manager Bud Black said. "He was making pitches as he went along. I was proud of him for battling. A lot of pitchers would have caved in there."
Bass' task grew tall in the first, when Hanley Ramirez drilled a three-run home run to left field, and three batters later, Giancarlo Stanton hit a two-run home run far into the Padres' bullpen beyond the center-field fence.
"It wasn't fun giving up five," Bass said.
However, Marlins pitcher Josh Johnson couldn't make it hold up. Johnson was gone after 2 2/3 innings, having allowed six runs on six hits with three walks with one hit batter.
The Padres led, 6-5, after three innings and later took a 7-6 lead in the fifth when Mark Kotsay had an RBI single. For Kotsay, he has six RBIs this season. All of them have given the Padres a lead.
Black said the Padres should know more on Saturday about Luebke's elbow and Street's shoulder. Street is scheduled to have an MRI exam on his shoulder.