Fernandez (3-1) outpitched Atlanta's Alex Wood (2-3), who also was dominant. Wood allowed four hits and one run with no walks and a career-high 11 strikeouts in eight innings.
The Marlins gave Fernandez the only run he would need in the fourth. Giancarlo Stanton hit a one-out double to left field and scored on Casey McGehee's single up the middle.
Fernandez struck out the side in the fourth and fifth innings. He allowed three hits with no walks.
Cishek pitched a perfect ninth for his fourth save.