Gayet, 41, had been nominated in the Best Supporting Actress category for her role as a ministerial adviser and seductress in Bertrand Tavernier's "Quai d'Orsay", a comedy about life at the French foreign ministry.
The award, however, went to actress Adele Haenel for her role in the film "Suzanne".
The revelation in January of Gayet's affair with Hollande, 59, prompted the end of the president's long-term relationship with Valerie Trierweiler, the country's de-facto first lady.
Organizers of the French film awards had earlier refused to be drawn on whether Gayet would be present or not at the ceremony and the actress skipped a traditional pre-awards dinner for nominees.
But Gayet, 41, ultimately ended the suspense, putting in her first high-profile appearance since news of the affair with the French president broke. The actress arrived at the awards ceremony at the Chatelet Theatre in central Paris on Friday wearing a black trouser suit with her long hair loose over her shoulders.