Wiggins finished the 41.5-kilometer (25.7-mile) run from Arc-et-Senans to Besancon in 51 minutes, 24 seconds.
The win upped his overall lead from 10 seconds to 1:53 over Cadel Evans of Australia, who placed sixth in Stage 9.
Wiggins' countryman Christopher Froome was second and Fabian Cancella of Switzerland third in the run to Bensacon -- a route that was mostly flat.
Froome was in third place overall, 2:07 behind Wiggins.
The Tour's first rest day will be Tuesday.