Fernandez had a 170-inning limit placed on him by the Marlins during his first season in the majors and he reached that in the fifth inning of his effort against the Braves. He wound up going seven frames, allowing a lone run on five hits.
He finished his rookie campaign with a 12-6 record in 27 starts and an earned run average of 2.19.
Twice this year he allowed just one hit over seven innings and his of 5.8 hits per nine innings is the best in the majors.
In the last of his 47 at-bats this season, Fernandez added to his memorable season by hitting a 1-0 pitch from Mike Minor over the wall in left to give the Marlins a 5-1 lead in the sixth.
Atlanta's only run off Fernandez came on a sixth-inning homer by Evan Gattis.
Giancarlo Stanton accounted for three Miami runs with an RBI single in the first and a two-run homer in the fifth.
Minor (13-7) suffered the loss, surrendering four runs on 11 hits in six innings.
With a win by Washington over the New York Mets Wednesday, Atlanta's magic number for clinching the National League East remained at seven.