Bastareaud, 29, apologised after the match but will face disciplinary action and, if found guilty, would face a minimum ban of six weeks.
The incident occurred in the last minute of a 36-0 Toulon victory in which Bastareaud scored a try.
He tweeted: "I want to apologise for my reaction to the player's insults."
The centre, who has won 42 France caps, added: "I reacted badly in responding to his provocation, I'm sincerely saddened that I could have hurt people."
During the game, former England fly-half Andy Goode condemned Bastareaud's comment.
He wrote on Twitter: "No place in the game for homophobia.
"Absolutely disgusting. I hope [tournament organisers European Professional Club Rugby (EPCR)] make an example of Bastareaud and ban him for a long time. Should throw the book at him."
A ban could put Bastareaud's chances of playing in the Six Nations at risk, with France's opening match against Ireland on 3 February.
In a statement on Sunday, EPCR said it "had received a citing complaint against the RC Toulon player, Mathieu Bastareaud".
It added: "Bastareaud is alleged to have verbally abused a Benetton Rugby player in the 80th minute of the match in contravention of Law 9.12.
"The complaint was made by the match citing commissioner, Dennis Jones (Wales)."