Sky teammate Christopher Froome finished second at 35secs with defending yellow jersey champion Cadel Evans way off the pace at 1min 43sec.
Team Sky leader Wiggins took a 10sec lead over Evans into the 41.5 km race against the clock between Arc-et-Senans and Besancon and clocked a winning time of 51min 24sec.
He now has a 1min 53sec lead over the Australian, who sits in second place, with Froome moving up to third at 2:07 behind Wiggins.
Armstrong sues USADA to end charges
Seven-time Tour de France champion Lance Armstrong filed a lawsuit yesterday in US District Court to stop US Anti-Doping Agency (USADA) officials from pushing forward with doping charges against him. The legal move, coming in the US cycling legend’s hometown, claims USADA rules are a violation of his US constitutional right to a fair trial and that USADA lacks jurisdiction in his specific case.