http://en.wikipedia.org/wiki/Supervillain
By some definitions, the first supervillain was John Devil, a proto-Fantômas, created by Paul Féval, père in his eponymous 1862 novel, or Féval's nearly-immortal, machiavellian Colonel Bozzo-Corona, leader of Les Habits Noirs introduced in 1863. Professor Moriarty, the archenemy of Arthur Conan Doyle's detective Sherlock Holmes, was introduced in 1891.[3] Dr. Fu Manchu, the antagonist of several popular novels of Sax Rohmer, is credited with popularizing many of the typical characteristics of the modern supervillain, including his sadistic personality, his desire for world domination, and his use of sinister lairs and themed crimes and henchmen. Rohmer's work had a strong influence on Ian Fleming, whose James Bond novels and their film adaptations further popularized the image in popular culture, like Ernst Stavro Blofeld.
The first supervillain who wore a bizarre costume was the Lightning, from the 1938 film The Fighting Devil Dogs. The first supervillain to regularly battle a superhero was the Ultra-Humanite, who first appeared in Action Comics #13 (1939). In contrast to the super-strong Superman, he was a crippled and bald genius, and could be seen as one of the first evil geniuses, due to his deformed body and baldness, which inspired Lex Luthor.
First one that came to mind was Fu Manchu but I assumed there were others before him. And he probably isn't the super powered type that you were after. Although according to his Wikipedia entry...
Dr. Fu Manchu has extended his already considerable lifespan by use of the elixir vitae, a formula he spent decades trying to perfect.