The 18-year-old was crowned by her countrywoman Dayana Mendoza, who won in 2008.
The first runner-up was Miss Dominican Republic, Ada Aimee De La Cruz. Miss Kosovo, Gona Dragusha, was named second runner-up. Rounding out the top five were Miss Australia, Rachael Finch, and Miss Puerto Rico, Mayra Matos Perez.
Miss USA, Kristen Dalton of North Carolina, was eliminated when the top 10 was trimmed to five.
As part of her victory package, Fernandez will have the use of a New York City apartment for a year, including living expenses, as well as a two-year scholarship from the New York Film Academy and a haul of fashion and beauty products.
The Public Chose, TooDuring the two-hour event, contestants from more than 80 countries and territories competed in three categories: swimsuit, evening gown and personality interview.
Billy Bush, co-anchor of Access Hollywood, and Claudia Jordan, a former Miss Rhode Island, hosted the event, which was televised in the U.S. on NBC and Telemundo. The 12-member judging panel included actor Dean Cain and supermodel Valeria Mazza.
Miss Thailand, Chutima Durongdej, was named Miss Photogenic Universe, an award voted on by the public at NBC.com and presented to the delegate who exemplifies beauty through the lens of a camera.
Miss China, Wang Jingyao, was named Miss Congeniality Universe, an award that reflects the respect and admiration of the delegate's peers.