Dyson (0-1) allowed seven runs on six hits and three walks while striking out only one in 2 2-3 innings.
"We're just trying to see what we have with these young guys," Marlins manager Mike Redmond said. "Up until today he's done a nice job in the bullpen. He'll bounce back and be ready for his next opportunity."
On a night when it seemed the Phillies' hitters couldn't miss at the plate, Dyson couldn't find it. Just 34 of 63 pitches he threw went for strikes.
"You can't give those guys free passes the way they swing the bats," Redmond said.
Lee (14-6) stroked a two-run, bases-loaded single to cap off a six-run third inning and also hit his first career triple in the fifth. Chase Utley, who also drove in four runs, hit a long three-run homer in the third.
On the mound, Lee allowed two runs while scattering eight hits and walking none, at one point retiring 11 straight en route to winning his fourth consecutive decision. The left-hander's 14 strikeouts marked his fourth double-digit strikeout game this year.
"Just being ahead in the count, pounding the strike zone, I had a lot of two strike counts," Lee said. "I'm really not trying to strike guys out in that situation to be honest with you. I'm just continuing to try to throw strikes, and that's what happens when you throw strikes."
Lee is 4-0 with a 2.05 ERA in his last six starts and 5-1 with a 2.29 lifetime ERA against Miami. He's also a career .391 hitter against the Marlins.
"Lee hurt us on both sides of the ball," Redmond said. "He knows how to pitch, moves the ball in and out. He got some runs early, so he could be more aggressive. ... He can hit (too). He give you good at-bats."
Philadelphia has won six in a row over Miami.
Utley got the Phillies started with an RBI groundout in the first. His 17th homer in the third gave them a four-run lead.
NOTES: In their last 29 games against the Marlins, the Phillies are 22-7. ... Dyson became the 12th different starting pitcher used by the Marlins this season, tied for most in the National League with the Mets and Pirates. ... Tuesday, Roy Halladay (3-4, 7.28) starts for the Phillies, while Brian Flynn (0-1, 10.13) goes for the Marlins.