The Los Angeles Lakers star's outburst was caught on camera as he reacted to being judged to have committed a foul.
Bryant is shown apparently mouthing the word "...faggot" after failing to get the referee's attention.
The player has apologised and said his action was out of "frustration in the heat of the game".
"What I said last night should not be taken literally," said Bryant, who also punched his chair and tossed a towel following referee Bennie Adams's call.
NBA commissioner David Stern said in a statement that Bryant's comment was "offensive and inexcusable".
"While I'm fully aware that basketball is an emotional game, such a distasteful term should never be tolerated. Accordingly, I have fined Kobe $100,000."
The Human Rights Campaign, a gay civil rights group, said Bryant's "horribly offensive and distasteful" language "perpetuates a culture of discrimination" and called for a fuller apology.
Bryant is one of the highest paid US sportsmen and one of US basketball's most celebrated stars.

The 23-year-old has scored six goals in 25 games since initially joining Wycombe on loan in July and has now signed a three-and-a-half-year deal.
Harriman, who is equally capable in defence or midfield, made just three first-team appearances for the R's.
"He's got everything you want from a professional," boss Gareth Ainsworth told the club website.
"He gives his all, he's got bags of ability and he's a great character to have around the club.
"To be able to keep him here is a fantastic piece of business and I'm grateful for the support of the board who have enabled me to make Michael a permanent signing."
Find all the latest football transfers on our dedicated page.
US basketball player Kobe Bryant has been fined $100,000 (£61,000) for using a homophobic slur during an NBA game on Tuesday.
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League Two side Wycombe Wanderers have signed utility man Michael Harriman from QPR for an undisclosed fee.