The PGA Tour said in a statement, "As he expressed after his round, we agree that Justin's comment was unacceptable."
He is likely to be fined for conduct unbecoming a professional, though the PGA Tour does not disclose conduct punishment.
A year ago, Scott Piercy lost two endorsement deals for sharing a homophobic meme poking fun at Democratic presidential candidate Pete Buttigieg, who is gay, when he announced he was suspending his campaign. Piercy also referenced the far-right conspiracy theory QAnon.
Patrick Reed also had to apologise in Shanghai in 2014 when he cursed in conjunction with a homophobic slur after three-putting.
Thomas, who reached No. 1 in the world for one week last year, is the defending champion at Kapalua.
"It's bad. There's no other way to put it," Thomas said. "I need to do better, I need to be better. It's definitely a learning experience. I just ... I deeply apologise to everybody and anybody who I offended and I'll be better because of it."