"I felt it on the last pitch of the fourth -- a slider to Domonic Brown," Slowey said. "I just kind of felt it grab a little bit underneath, kind of my left [scapula] area."
After winning the series opener, Miami dropped the final two games against Philadelphia, ending its homestand with a 2-7 record.
As the Marlins saw their starting pitcher leave the game, Phillies left-hander Cliff Lee stayed for the duration in a dominant outing. He recorded his 12th career shutout, limiting Miami to three hits and striking out five.
Two of the Marlins' three hits were infield singles.
"Outstanding. Real good," Philadelphia manager Charlie Manuel said. "In the last part of the game, when he got ahead of the hitters, he was making them all hit the ball to right field. That's good. That's how you finish the game and keep your pitch count down. They were hitting the ball in the air to the opposite field."
Marlins manager Mike Redmond added: "He was on tonight. He was on, and he threw some tough pitches."
Slowey said he threw mostly fastballs in the fifth while dealing with the discomfort and decided to end his night after feeling the ailment while warming up prior to the sixth.
The right-hander will be re-evaluated Thursday.
"My hope was to go back out to throw the sixth and beyond. My pitch count was pretty low," Slowey said. "But I didn't want to go out there and not be able to give my team a chance to compete."
Aside from the injury, Slowey's outing was a return to form. He gave up on one run on six hits, striking out six and walking none. In his previous two starts, he surrendered 11 runs on 18 hits in 7 2/3 combined innings.
"I felt a whole lot better mechanically," Slowey said. "I was able to stay over the rubber longer and had a better angle on pitches that came in."
"His last couple of outings, he's been a little bit off," Redmond said. "But he was on tonight. I would have loved to see him go out there for the next couple of innings, but that's part of it. He felt that side, and we had to make sure we get him out of there. We're going to need him for the long haul."
The lone blemish on Slowey's line came courtesy of the Phillies' Delmon Young.
Young homered for the second consecutive night, belting an 0-2 sinker from Slowey over the wall in left-center field with two outs in the fourth to give Philadelphia a 1-0 lead.
"I obviously made a mistake to Delmon," Slowey said. "I left the ball back over the plate. [On] 0-2, he's a guy that's swinging and can put a charge into the ball. Been swinging well lately. That's one of the pitches I'd like back."
The Phillies had threatened with leadoff singles in the first three innings, but Slowey worked his way out of trouble each time.
Following Slowey's departure, Philadelphia added two runs in the sixth against left-hander Wade LeBlanc on RBI hits by Domonic Brown and Freddy Galvis.
The Marlins, too, made an early offensive push, loading the bases against Lee with no outs in the bottom of the second.
After giving up a leadoff infield single to Marcell Ozuna, Lee walked Justin Ruggiano and hit Chris Coghlan with a pitch. Lee had only 11 walks in 63 2/3 innings before Wednesday, and Coghlan was the left-hander's first hit batsman since plunking Giancarlo Stanton on Sept. 15, 2011.
But the rally died soon after it began.
Nick Green grounded into a 5-2-3 double play and Jeff Mathis followed with a popout to second base.
"We had the bases loaded, had that one opportunity to score, and we didn't get it done and that's about it," Redmond said.
Green's double play marked the continuation of a season-long issue for the offense. The Marlins had grounded into 46 double plays before Wednesday, tied for the NL lead with the D-backs. The Angels led the Majors with 47.
Miami's offense did not muster much after the second inning, notching only two more hits -- a leadoff single by Miguel Olivo in the sixth and a two-out single by Derek Dietrich in the ninth -- the rest of the way.
"They got the big hits," Redmond said. "We didn't."