Headley, fresh off the disabled list after missing 14 games, punctuated a four-run sixth inning with his three-run blast off reliever Carlos Marmol. All the damage in the inning came with two outs and none on. Everth Cabrera started things off with a bunt single.
"I wish the outcome could have been a little bit different," McGehee said. "All things considered, we've got a huge game tomorrow to try to split this four-game series and get us on the way for a long road trip.
Smith was a single shy of the cycle, and in the first three games of the series, he has three doubles, two triples and a homer.
It's was a rough loss for the Marlins in a number of ways. They fell out of a tie for first place with the Braves in the National League East, and once again the bullpen struggled. Marmol, especially, has endured a tough time.
Postgame, the team announced Marmol will be designated for assignment on Sunday, with a corresponding move to follow.
"It's been a struggle for him," manager Mike Redmond said. "We've tried to keep getting him in there in different situations. It just hasn't worked."
The Padres, after losing 3-1 on Thursday, stormed back to take the next two with big offensive displays. San Diego hadn't scored more than six runs all season before winning, 10-1, on Friday. Eric Stults, who limited Miami to two runs in six innings, collected Saturday's win.
"They are aggressive," Stults said. "That first inning, they were swinging early. That first-pitch [fastball] to McGehee, I got hurt. But after that, I was able to make pitches down in the zone a lot more."
Miami starter Nathan Eovaldi allowed two runs in five innings, but he labored in every inning and exited after 112 pitches.
"You don't want to throw 112 pitches in five innings," Eovaldi said. "Every at-bat was like a struggle. When I did get quick outs, it was falling behind. Two-out walks, that just can't happen. We put up two early, you've got to put up zeros."
Eovaldi came into the game having walked six in 45 1/3 innings. He walked four Padres, while allowing seven hits.
In each of the first five innings, the Padres stranded runners in scoring position.
San Diego chipped away at Eovaldi's pitch count, running it up to 66 through three innings, and 89 through four.
As much as he labored, Eovaldi kept making the necessary pitches to prevent further damage.
"It's tough when our guys come out and score two early, and then to go out there and give one up in the first," Eovaldi said. "I was just battling myself out there. Everything wasn't feeling too good. Fastball, I wasn't locating it. I was falling behind in counts. Not getting first-pitch strikes. It's hard to pitch like that."
Early on, it appeared the Marlins would be in good shape. Before throwing a pitch, Eovaldi was handed a two-run lead, courtesy of McGehee's homer.
On his 137th at-bat of the season, McGehee posted his first home run. The drive to left-center was estimated at 417 feet.
McGehee, who played in Japan last year, connected on his first shot since Aug. 11, 2012, when he was with the Yankees against the Blue Jays.
Not unexpectedly, McGehee was given the silent treatment when he entered the dugout.
"I was pretty sure it was coming, so I wasn't too surprised," McGehee said. "It was kind of bittersweet. I wish things would have turned out different. We've got to wash this one off quick and get back at it tomorrow morning."
Reliever Carter Capps gave up an RBI single in the eighth to Yonder Alonso, who reached base five times (three singles, two walks) for the Padres.
The Marlins added their third run in the seventh inning when Jeff Baker doubled and scored on Reed Johnson's double.
But the night for the Marlins at the plate was marred by another high strikeout total. The Padres combined to strike out 12, raising their total to 39 in the series.
"We're still striking out way too much," Redmond said. "We've just got to figure this thing out. We'll come out tomorrow and try to find a way to get a win, whether it's a great pitching performance or a big hit, or a few big hits. That's what we need. I know the guys are battling. I know the effort is there. We probably need to relax a little bit and go out there and play the game and have some fun."