New York collected back-to-back singles to start the frame before Cishek struck out Ike Davis. Lucas Duda drove in a run with a single that put runners at the corners. Mike Baxter fouled out to shallow left and Andres Torres walked after taking a few close pitches to load the bases.
Kelly Shoppach then lined a single to center that got under the glove of Justin Ruggiano for his third error of the year, clearing the bases. Prior to the at-bat, righties were batting just .160 against the sidearming Cishek.
It wasted Josh Johnson's eight-inning effort, in which the ace allowed one run on three hits over 105 pitches. He bounced back from one of the worst starts of his career, which came last Saturday against the Dodgers when he surrendered six runs on 10 hits in three innings.
The right-hander showed flashes of his former self, tossing a 10-pitch first inning and never looking back, giving up no hits through four and permitting just a leadoff walk to Davis in the second.
According to Johnson, he changed a few things in his delivery since his last outing, including closing up his front side a little longer in order to hide the ball.
"I've pitched pretty well, made a couple of bad pitches, but other than that, it was a good outing, positive outing," said Johnson, who had lost four starts in a row in one season for the first time and hasn't won since Aug. 3. "I got deep in the game, which was my goal in the first place."
Giancarlo Stanton, known for his power, produced the then-go-ahead run with a dribbler off the end of his bat against starter Jeremy Hefner with runners on the corners and one out in the sixth inning.
Jose Reyes, who got things started, raced to third on Carlos Lee's bloop single into right field. Stanton's first-pitch swing rolled along the infield grass, and he beat Davis' toss to Hefner, who covered first.
"It's my responsibility to go back there," said Hefner, who earned the no-decision after six innings of two-run ball. "It's my fault on the play. I should've gone to the bag there. I picked it up and I thought he was going to go home, but obviously Jose is a fast runner. I should've been at the bag."
Miami added a run in the eighth off Ramon Ramirez to make it 3-1 on Lee's RBI single to center that scored Reyes, who walked with one out and stole his 30th base of the season, the 400th of his career.
The Marlins scored in the third when Donovan Solano, whose career-high 12-game hitting streak was snapped Friday night, prevented Ruben Tejada from turning a double play on John Buck's grounder to short by moving on a full-count pitch.
Following a Johnson strikeout, Bryan Petersen connected on the first pitch from Hefner, drilling the ball to left-center past a diving Torres for a two-out RBI double.
Baxter's leadoff double to left sparked a New York rally in the fifth. He moved to third on Torres' grounder to second and scored on Josh Thole's grounder to short -- despite the infield playing in -- knotting the score at 1.
Frank Francisco earned his 23rd save with a perfect ninth.
"That's the way we've been all year long," Marlins manager Ozzie Guillen said. "The starters go out there and have a great day once in a while, and some we can't hold the lead. I think we played well. We just got beat in that inning, and [when] you get beat, you just have to erase [it] because you can and be ready for next game."