The South Florida Sun-Sentinel first reported the incident.
Garrett was scheduled on Monday to be examined in Miami by the Marlins' team hand specialist, Dr. Patrick Owens.
"It was a prank gone bad," Marlins president of baseball operations Michael Hill told MLB.com on Monday. "These guys are very good friends. Roommates. Josh, trying to pull a prank on his friend and teammate, made a horrible mistake."
Hill said Naylor served a one-game suspension and was levied a small fine, but he's back playing for the Grasshoppers.
"There was a small suspension while we're investigating everything," Hill said. "If it's more serious, or we think that we need to take further action, we still will. But it was a one-game suspension, pending further investigation."
The incident reportedly occurred at their Greensboro apartment.
According to MLBPipeline.com, Naylor is the organization's No. 2 prospect, and Garrett is No. 4.
Naylor, a left-handed-hitting first baseman, is batting .262 with seven homers and 36 RBIs this season.
Garrett is a promising outfield prospect who has speed and power. An eighth-round pick in 2014, he's hitting .244 with five home runs and 15 RBIs. In 133 Minor League games, Garrett is batting .265/.316/.455 with 16 home runs and 72 RBIs.
"We're waiting to hear back on [Garrett's examination]," Hill said. "Hopefully, it's nothing too serious, and we'll get him back to continue his development towards the big leagues."
Joe Frisaro has covered the Marlins for MLB.com since 2002. 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.