All four runs Marquis surrendered were unearned. They marked the only blemishes on his 6 1/3 strong innings, which netted Marquis his fifth quality start in his past six outings. Marquis didn't allow a hit until Adeiny Hechavarria led off the fifth with a single.
"I thought I threw the ball well," Marquis said. "Not the results you want. A lot of times, you come out with a loss, it's not a good day. I feel if I keep throwing the ball like that, then there'll be more W's than losses."
"He hung in there. He had a no-hitter through five innings. That was a game where that is pretty typical of Jason's performances all year. He hung in there," said manager Bud Black.
The Marlins' Ed Lucas led off the sixth with a routine grounder to shortstop, but managed to reach base by way of a Pedro Ciriaco throwing error. Kyle Blanks jumped to corral the errant throw, coming off the bag.
"I just rushed a little bit and just made a bad throw," Ciriaco said. "I've just got to do a better job next time. ...
"When you make a mistake or an error, that play is never going to come back. You've got to be focused and make the next play."
"He's been around. He'll be fine. He made two great plays prior to that. That was a situation where he had to hurry a little bit and just made a high throw," said Black.
Ciriaco's defensive misstep came shortly removed from two outstanding, run-saving plays during the fourth and fifth innings.
With two on and one out in the fourth, Marcell Ozuna hit a line drive between third and short. Ciriaco dove to his right and snagged the liner, helping preserve the scoreless tie.
One inning later, Marquis again faced trouble with runners on the corners with one out and Justin Ruggiano at the plate. Ruggiano hit a grounder to short, and Ciriaco began to fall once he fielded the ball.
Ciriaco fired a strike to Logan Forsythe from the dirt, who made a strong throw to first and completed the inning-ending double play.
Ciriaco's two highlight-reel plays kept the contest scoreless into the sixth, but his throwing error kick-started an explosive frame from the Marlins.
After Lucas reached, Giancarlo Stanton walked and Logan Morrison was retired on a flyout to left, setting up Ozuna's second at-bat of the night with runners in scoring position.
Ozuna singled over Forsythe's head into right-center and plated Miami's first run.
Following an intentional walk of Derek Dietrich and a swinging strikeout of Hechavarria, only Jeff Mathis stood between Marquis and escaping the inning with minimal damage.
Just one day after his walk-off grand slam in Sunday's 6-2 Miami victory, Mathis crushed San Diego with another big hit, clearing the bases with a three-run double off the left-field wall.
Mathis, who entered the four-game series batting .109 with one home run and five RBIs, went 4-for-10 with a homer and nine RBIs in three games against San Diego.
"You've got to make pitches," Marquis said. "That's really what it comes down to. They're still big league hitters. They still hit mistakes. [Mathis] had a plan, and he executed it and that was the game."
While Mathis supplied Miami with three critical insurance runs, Fernandez would have been fine with only Ozuna's run-scoring single.
The 20-year-old hurler gave up only two hits and walked one while matching his career-best 10 strikeouts and pitching a career-high eight innings. For the sixth consecutive outing, Fernandez surrendered two earned runs or fewer.
Fernandez also became the first pitcher to two-hit the Padres since Vicente Padilla accomplished the feat as a Dodger on August 4, 2010.
San Diego's only two hits against Fernandez -- a first-inning Carlos Quentin double and a seventh-inning Blanks single -- came 19 batters apart, a streak of outs only interrupted once by a full-count walk to Forsythe in the third.
"He's got a good arm, and he's a very talented 20-year-old pitcher," Black said. "He's a guy that, when you break him down, he does a lot of things right. And for 20, he's advanced, really is for a 20-year-old.
"He's got a good delivery, repeats it. He can spin a breaking ball. That's a very good breaking ball. One of the best breaking balls I've seen this year. A very good, tight breaking ball with great spin."
Fernandez was the third of three young Marlins pitchers to take the hill and defeat the Padres, clinching the four-game series after a loss in Friday's opener.
Right-handers Jacob Turner (22), Nathan Eovaldi (23) and Fernandez (20) combined to give up only one run on 13 hits with five walks and 17 strikeouts in 23 innings.
The 20-somethings handed San Diego its third series loss in its past four and dropped the Padres down from second to third in the National League West.
"They've got a nice grouping of young guys," Black said. "They've got to be really happy with those guys. They've got them in the big leagues. They're gaining experience. They've got velocity. They pitch with the fastball, which is, I think, very important for a young starting pitcher to be able to pitch with the fastball."
"The three young guys that they have are pretty impressive. Pretty good young arms, and I think they've got a good base to keep them good for a few years here," said Marquis.
Joe Morgan is an associate reporter for MLB.com.
This story was not subject to the approval of Major League Baseball or its clubs.