The reigning NL Rookie of the Year gave up five runs in nine hits in 4 2-3 innings, struck out three and walked two. His next outing will be in Monday's opener at home against Colorado.
''It's not like I can put the ball where I want to every time,'' Fernandez said. ''We'll see what happens in six days and go from there.''
Marlins manager Mike Redmond wasn't overly concerned.
''You can tell he was having to really grind it out out there and wasn't quite as sharp with his pitches,'' Redmond said. ''He tried to limit the damage. Overall, he got his pitches in and can move on.''
Cardinals starter Lance Lynn struck out eight and walked one in five innings, giving up three runs and five hits.
Juan Diaz hit his first spring-training homer and drove in two runs for the Marlins, who rallied from a 5-3, seventh-inning deficit. Casey McGehee hit his second exhibition homer for Miami, which is 5-0 against the Cardinals this spring training.
There was a 46-minute rain delay after the top of the sixth.
Cardinals: Lynn threw 59 strikes among 91 pitches. He started in three of the Cardinals losses against Miami this spring training.
Marlins: Fernandez threw 58 strikes among 98 pitches. he had a 3.54 ERA in spring training over 20 1-3 innings.
Marlins: Outfielder Reed Johnson, at spring training on a minor league contract, was told he is being added to the major league roster. Under baseball's labor contract, he had to be notified by noon on Tuesday he will be added, be given a $100,000 retention payment or be released.
Right-handers Arquimedes Caminero and Carter Capps were optioned to Triple-A New Orleans. Right-hander Chaz Roe was reassigned to minor league camp.
Caminero allowed two runs during nine innings in spring training, striking out nine and walking one.
''It's tough that I'm going down,'' a disappointed Caminero said. ''I'm going to keep working hard, try to do what I've been doing and let them make the decision. (They said) I did nothing wrong, and that it was a tough decision for them.''
Infielder Ty Wigginton, in camp on a minor league contract, was released.
''It was tough telling a guy who has been around for a long time that it's not going to happen this year,'' Redmond said.
Marlins: Rafael Furcal, hindered by a hamstring strain, is not certain whether he will be ready for the opener.
Furcal played in his second straight minor league game as a designated hitter Tuesday.
''We're still waiting on Furcal,'' Redmond said. ''We'll probably slide him into a game out here in the next couple of days. We definitely need to see him play in a regular game and see how that leg is feeling.''
If Furcal isn't ready, Derek Dietrich, Donovan Solano and Ed Lucas are options at second. Adeiny Hechavarria left Monday's game in the fifth inning with a mild groin strain and the Marlins plan to rest him until Friday.
MARINO WILL BE IN THE HOUSE
Former Dolphins Hall of Famer Dan Marino will throw out the ceremonial first pitch at the Marlins' opener.
Peter Bourjos said recently playing center field has been boring during spring training because very few fly balls have been hit there off Cardinals pitchers.
''Overall, we haven't got to see his range and that's a good thing,'' Cardinals manager Mike Matheny said. ''We'd rather not see his back running to the fence all the time.''