The lone run Fernandez allowed was a home run to Michael Ratterree in the second inning.
Originally, Fernandez was slated to pitch on Wednesday for Triple-A New Orleans at Round Rock. But due to inclement weather conditions in Texas, Miami rescheduled and had its ace throw for Jupiter.
Fernandez is scheduled to make two more rehab starts, on June 22 with Jupiter and on June 27 with Double-A Jacksonville.
After that, the 22-year-old will return to Miami's rotation on July 2.
Fernandez underwent Tommy John surgery on May 16, 2014, and the 2013 National League Rookie of the Year last saw big league action last year on May 9 at San Diego.
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter @JoeFrisaro and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.