"It felt real good," Eovaldi said. "For the most part the fastball was there. Later in the game I was falling behind the batters a lot (but) I was able to make my pitches when I needed to behind in the count and the defense was there."
Eovaldi (4-6) allowed three hits over 7 2-3 innings. He struck out five and walked two.
"Our offense came up short against a pitcher who really kept his stuff all the way through his outing," Phillies manager Ryne Sandberg said.
Eovaldi will make his final start on Saturday against Detroit.
"These last few starts and hopefully finishing up on a good note, is going to be big for next year," Eovaldi said.
Justin Ruggiano drew a bases loaded walk in the first inning and the Marlins scored three runs in the eighth on RBI singles by Donovan Solando and Ed Lucas and a sacrifice fly by Christian Yelich.
"We've had a long couple of days," Marlins manager Mike Redmond said. "With the double-header (Sunday) and getting back at 4 in the morning, that's exactly what we needed."
Roy Halladay (4-5) left the game with right arm fatigue after walking two of the first three batters he faced. He threw five strikes in 16 pitches before Sandberg visited the mound and removed Halladay.
"Really, the last few starts I just haven't been getting that bounce back in between," Halladay said. "I have zero pain which is good, but talking to the doctor he said I just need rest."
"Doc obviously wasn't himself out there," Sandberg said.
Halladay, who had shoulder surgery on May 15 and returned to the mound on Aug. 25, is not planning to make another start this season. The 36-year old two-time Cy Young Award winner will be a free agent in the offseason.
"I don't know what the future is going to hold, but I want to go somewhere that wants me and somewhere that is going to have a shot," Halladay said. "Like I've always told you guys, I hope that's here. Worst-case scenario I start throwing and things aren't happening the way they're supposed to, then I'm going to be honest with whoever is interested and make a decision from there. But if things go the way I've been told they're going to go and the way I expect them to go, I'm going to be able to be competitive next year. I've never given up the hope that I could pitch here again."
Luis Garcia relieved Halladay and walked the first two batters he faced -- including Ruggiano -- to give the Marlins a 1-0 lead.
Philadelphia used seven pitchers and they combined for nine walks.
"We patched it up and the bullpen actually did a fine job keeping it a 1-0 game into the eighth," Sandberg said.
Eovaldi issued a two-out walk to Cesar Hernandez in the eighth that ended his night. Mike Dunn came on to get the final out of the inning and Steve Cishek pitched the ninth.
Solano and Lucas hit consecutive RBI singles with the bases loaded off B.J. Rosenberg in the eighth and Yelich added a sacrifice fly.
NOTES: Halladay is 55-29 with a 3.25 ERA in four seasons with the Phillies. ... Adeiny Hechavarria had two hits to give him a team-high 32 multi-hit games. ... Philadelphia RHP Kyle Kendrick was placed on the 15-day DL with right shoulder tendinitis, retroactive to Sept. 14. ... Miami RHP Henderson Alvarez (4-5, 4.05 ERA) will face Philadelphia RHP Zach Miner (0-1, 3.22) on Tuesday.