The United States Anti-Doping Agency accused the 41-year-old of running "the most sophisticated, professionalised and successful doping programme the sport has ever seen" during his career.
Despite Armstrong's innocent stance, 11 of his former US Postal Service teammates testified against the cyclist, who was stripped of his record seven Tour de France titles after refusing to fight the doping charges against him.
Barton tweeted: "I am really surprised by Nike decision to stand by him. Through it makes a change for a major brand, it does seem a little ill judged. Considering the mountain of evidence presented against him by the stirling work of the Usada."
Armstrong was also handed a lifetime ban earlier this year.