Moments before, the Marlins paid tribute to 24-year-old Jose Fernandez, who was killed in a boating accident Sunday morning.
Gordon, who called Fernandez "family" in a tribute on Instagram, wore Fernandez's helmet when he hit the home run.
It was Gordon's first home-run of the year.
Prior to the game, Gordon was wearing a t-shirt emblazoned with "R.I.P." with the "I" replaced by a photo of Fernandez during.
Gordon, a left-handed hitter, took his first pitch batting right-handed in memory of the right-handed Fernandez.
Gordon cried as his teammates hugged him in the dugout, who were all wearing number 16 in memory of Fernandez.
Watch Dee Gordon tear up after leading off with home run:
Chills as Dee Gordon leads off with HR for @Marlins on an emotional night. #JDF16 #MLB @FOXMarlins pic.twitter.com/gwAbShjliZ