The alleged beating on Tuesday has prompted a heated political debate over whether France is falling prey to "religious fundamentalism and ghettoised communities".
The incident took place less than a week before football fans arrive in the French Riviera town for a Euro 2016 match between Poland and Northern Ireland.
The two men have reportedly been identified. One of them is known to be an illegal migrant who is a notoriously threatening figure in the district, but both are currently at large.
The waitress, who works at the Vitis Cafe in central Nice, said: "I'm so scared. Why did they insult me? I feel debased, humiliated, sullied. I don't want other women to have to be victims of such an attack.
"It's not because I serve alcohol that I'm not fulfilling my [religious] duty, I do it because I'm a waitress," she told Nouvel Obs, a French magazine.
The waitress has filed a police complaint for "voluntary violence".
This is not the first time the district has seen such "religious" threats. In October 2014, three men, including the owner of a Halal store - since forcibly closed by police - threatened a baker who sold ham sandwiches, saying he wasn't a "good Muslim".
This latest incident caused angry reactions from right-wing politicians who saw it as a sign that the country's values were being undermined. The issue has become increasingly fraught less than a year before presidential elections and six months after Islamist attacks in Paris killed 130.
Eric Ciotti, MP with the Republicans, Nicolas Sarkozy's conservative party, said: "This attack should be placed in a national context that has seen a constant rise in religious fundamentalism and ghettoised communities.
"Each attack like this strikes a severe blow against the values of the French Republic."
Philippe Vardon, regional councillor with the far-right Front National (FN), said: "This situation comes from the weakness of our political leaders."
FN leader Marine Le Pen is polled to reach the second round of presidential elections next year and has repeatedly claimed that France is becoming prey to "creeping Islamisation".