Isaac also opted to not don the Black Lives Matter shirt that all other players wore for the protest. When asked about his decision postgame, he said he "absolutely" believes in the social justice movement.
"I believe that Black Lives Matter. A lot went into my decision, and part of it is that, first off, it's my thought that kneeling while wearing a Black Lives Matter T-shirt don't go hand in hand with supporting Black lives," he said, according to The Athletic's Clevis Murray.
All coaches from both clubs also knelt in protest, with some players choosing to lock arms as others raised a fist.
Isaac cited his religious beliefs in choosing not to participate.
"I believe Jesus is the answer. I didn't think wearing a message on the jersey was the answer," he said, according to ESPN's Marc J. Spears, adding he took the time during the anthem to pray.
Magic head coach Steve Clifford says he and the rest of the team backed Isaac's choice not to take part in the display.
"We are all supporting each other in this, and if guys are not comfortable kneeling and they want to stand then nobody has a problem with that," Clifford said, courtesy of FOX Sports Magic. "I support him, his teammates support him, the organization supports him, so that's part of living in our country."
Isaac finished the game with 16 points and six rebounds in 16 minutes as the Magic won 128-118.