The Phillies have lost five straight and are 36-45.
"There's nothing you can take away from this series," Phillies left fielder Juan Pierre said. "You just forget about it. The second half of the season is right upon us now."
Ricky Nolasco (7-6) pitched seven strong innings and Hanley Ramirez hit a two-run home run for the Marlins, who swept the Phillies for the first time since August 7-9, 2009, at Citizens Bank Park.
"We are trying to beat everybody, but especially in our division," Ramirez said. "If you want to move up, that's what you have to do."
The two-run home run by Ramirez, which put the Marlins up 5-2 in the eighth, ended a drought of 89 at-bats without a homer.
"We've been waiting for Hanley's big day," Marlins manager Ozzie Guillen said.
All-Star slugger Giancarlo Stanton also homered, and Omar Infante and John Buck each hit RBI doubles for the Marlins, who are looking to put an 8-18 June behind them, have won four straight.
"June, get far away from us," Stanton said. "It's good to start new and just move forward."
Nolasco struck out six as he scattered five hits and allowed two runs.
"A sweep against anybody is big, but we know how good that team is and we're trying to prevent them from getting on a roll as well," Nolasco said.
Nolasco improved to 8-4 with a 3.59 ERA over 14 starts against the Phillies.
"He's always been a better pitcher than people give him credit for," Phillies manager Charlie Manuel said. "I've seen him pitch some real good games over the time I've been here."
With the Marlins leading 3-2 in the top of the eighth, Steve Cishek allowed two singles before getting Shane Victorino to fly out to end the inning.
Ramirez's homer came off Antonio Bastardo.
"The biggest hit today was the home run by Hanley," Guillen said. "Hanley opened up the game a little bit to give you some room for a mistake."
Ramirez said: "It was good for the crowd."
Heath Bell came on in the ninth for his 17th save in 21 chances.
Philadelphia starter Joe Blanton (7-7) allowed three runs and six hits in six innings. He struck out seven.
"If we go out and throw a good game, we have trouble scraping across a couple and that's just baseball," Blanton said. "Sometimes it goes that way."
After Pierre tripled and scored on a groundout by Carlos Ruiz, Miami took a 2-1 lead on consecutive RBI doubles by Infante and Buck.
Stanton's third home run in five games - his 19th overall - gave Miami a 3-1 advantage in the third. Nolasco, who had retired 11 straight at one point, was charged with two wild pitches in the sixth, which resulted in the Phillies' second run.
NOTES: The Phillies have had at least three All-Star selections in four consecutive years as LHP Cole Hamels, RHP Jonathan Papelbon and C Carlos Ruiz were selected to represent the National League on July 10. ... The Phillies selected the contract of OF Jason Pridie from Triple-A Lehigh Valley to fill the roster spot available after trading 1B Jim Thome to Baltimore. ... Marlins RHP Carlos Zambrano (4-6, 3.71 ERA) will start Monday against Brewers RHP Zack Greinke (9-2, 2.82 ERA). Phillies RHP Vance Worley (4-4, 2.92 ERA) will face Mets LHP Jonathon Niese (6-3, 3.55 ERA) on Tuesday.