Hilary Swank in Boys Don't Cry (1999) - won
Salma Hayek in Frida (2002) - nominated
Nicole Kidman in The Hours (2002) - won
Charlize Theron in Monster (2003) - won
Mo'Nique in Precious (2009) - won
While this seems like a recent trend, it has happened in the past. Certain classic film actresses chose to strip their makeup and expose themselves to the harsh unforgiving lens of the movie camera in order to honor their character's role in the film. One that comes to mind is Norma Shearer in Marie Antoinette (1938). Yes I know it's one of her "prestige" films and she donned wigs, makeup and fabulous period costumes throughout the film. But at the end of the movie, when Marie Antoinette is imprisoned and about to be beheaded, there is a poignant scene with Norma Shearer, sans makeup and with a worn and fearful expression on her countenance all of which makes you forget that she is the Queen of MGM.
The best example I can think of, of a classic film actress undergoing a dramatic physical transformation is Bette Davis in The Private Lives of Essex and Elizabeth (1939). Davis was determined, at all costs, to look the part of Queen Elizabeth I. And in a time when historical pictures were frivolous with facts and details, it's admirable to see how devoted Davis was to being as historically accurate as possible.
From the book, Fasten Your Seat Belts: The Passionate Life of Bette Davis by Lawrence J. Quirk
[Makeup artist] Perc Westmore... shaved Davis's hair back two inches, thus underlining the reality of baldness under the red wigs and hairpieces. He then applied white, pasty makeup and shaved off her eyebrows, replacing them with thin lines that, in Robert Lord's words, 'made her look like a baby in a Halloween mask and costume.'
Davis spent much time studying portrait reproductions provided by the research department, seeking to approximate Elizabeth's actual appearance as accurately as possible. Her own appearance meant nothing to her - only historical accuracy. 'Make me up horribly, and dress me outlandishly - I don't care, so long as you get the essence of the original,' she told Perc Westmore and [costume designer] Orry-Kelly.
Yet Bette Davis didn't win the Oscar for this performance. She wasn't even nominated for it. Instead, the Academy favored her performance in Dark Victory (1939) more and she was nominated for that role. If Bette Davis had done the same two performances in today's day and age, would she have won for Private Lives of Essex and Elizabeth instead?