The pitch barely glanced off Peralta's right shoulder before it hit his helmet near the ear hole. Fernandez immediately put his hands on his head as he slowly walked toward home plate, in front of which Peralta laid facedown for a couple minutes.
"When the ball came out of my hand, I knew it was a really bad pitch," Fernandez said after he spent several minutes outside the Marlins clubhouse trying to get in touch with Peralta following the game. "I was just hoping for him not to get hit. I was not too happy about that.
"I was trying to go in, and it's sad because I know the kid personally, No. 1, and No. 2, you never want to hit anybody in the head. That's the last thing you want to do as a pitcher. It's really scary. I got really scared because that's not something nice to see."
Peralta eventually walked back to the home dugout under his own power, replaced by a pinch-runner, and after the game said he will be OK. Fernandez struck out fellow Cuban Yasmany Tomas on three curveballs to end the inning but still was visibly shaken by the play and received what looked like a pep talk from Mat Latos between innings.
"It wasn't easy [to finish the inning]," Fernandez said. "Not fun. It was really tough.
"It's just something you don't want to see. The big picture is the team won but it's something you don't want to see. It's not good for the game. I would never want that to happen to anybody, myself, my teammates, anybody who plays the game."
Fernandez and Peralta know each other through Martin Prado, who played with the D-backs in 2013 and the first half of last season, and hung out in Miami earlier this year.
"That was a scary moment," Peralta said. "As soon as I saw the ball out of his hand, I saw it right in my face. I'm trying to protect myself. ... It still got me good on my ear. That first moment when I landed on the ground, I was so scared, but it happens."
D-backs reliever Dominic Leone hit Christian Yelich in the hip area an inning later and immediately was ejected.
"The Diamondbacks handled it the right way," Marlins manager Dan Jennings said. "It's part of baseball. They hit Yelly in a spot that sent the message; that's part of the game."
Fernandez (3-0) threw a season-high 97 pitches in seven innings, and the 11 strikeouts were the most since he struck out 14 Braves on April 22, 2014.
"Jose set the tone with outstanding stuff," Jennings said. "That's a good hitting ballclub and for Jose to go out there and battle through seven, that certainly was huge."
Fernandez gave up three runs on five hits and a pair of walks. He also had a run-scoring, ground-rule double in the second, and after he reached on an error in the fifth, he scored from first base on an Ichiro Suzuki triple.
"I feel pretty healthy. I feel real normal," he said. "I feel, I don't want to say like I was before [Tommy John surgery], but I feel like I have grown as a pitcher."
Chris Gabel is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.