Right-hander Kevin Slowey will pitch Miami's "B" game on Monday.
"There's really no reason for him to go and face the Mets again," Marlins manager Mike Redmond said of Fernandez. "He'll get plenty of opportunities to do that during the season."
Fernandez has drawn the Mets many times during his short time in the Majors. He made his Major League debut against New York last April and faced them four times in his first 12 starts last season, including two straight outings in early June.
No other NL East opponent faced Fernandez more than twice in 2013.
The 21-year-old also pitched a perfect inning of relief with two strikeouts at Citi Field during the 2013 All-Star Game.
Joe Morgan is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.