Fernandez, who threw 76 pitches in five innings on Friday against the Braves at Turner Field, returned to Miami on Saturday, where he was examined by team physician, Dr. Lee Kaplan. At the time, the club was calling his ailment "right shoulder stiffness."
The fact there is no structural damage is reason for encouragement.
The Marlins are expected to call up left-hander Justin Nicolino from Triple-A New Orleans to start against the Red Sox on Tuesday.
Fernandez, who missed nearly 14 months due to Tommy John surgery, rejoined the rotation on July 2. In seven starts, he's 4-0 with a 2.30 ERA in 43 innings.
Ideally, the club would like to see him back on the mound before the season ends.
"When I spoke with Jose this morning, I think he definitely has peace of mind as to, 'What now?'" manager Dan Jennings said. "Hopefully, the inflammation will get out of there and we can get him healthy, and get him back."
Since coming back, the Marlins have taken a "common sense" approach with their young ace. He threw 112 pitches against the Padres on Aug. 2, and followed that up with his 76 pitches on Friday, including a 38-pitch fourth inning.
"Now that we have it identified, I think we'll have a better understanding on how exactly to treat it," Jennings said. "I'd like to see him pitch. I think he wants to pitch, in talking to him this morning."
Fernandez's velocity reached as high as 98 mph on Friday, which he touched three times. His final pitch of the night was a 94- mph fastball.
One reason Fernandez is so dominant is he commands four pitches, fastball, slider, curveball and changeup. Of the 76 pitches he threw on Friday, according to MLB.com's Gameday tracking, 38 were fastballs (either two or four seam) and 27 were breaking balls (slider or curve), plus 11 changeups.
In his 38-pitch fourth, he threw 18 breaking pitches, 15 fastballs and five changeups.
Miami is in last place in the National League East, and the club has no reason to rush Fernandez back.
"Now we have to be smart of where we are in this season," Jennings said. "He's worked extremely hard. You know how competitive he is. But we won't do it until we know he's back 100 percent. There is no need to push it or rush it."