Liquigas rider Nibali, who is fourth in the overall standings, broke away in the descent from the Col du Grand Colombier and built a one-minute lead over Wiggins, but the Briton's Team Sky easily reined him in before the line.
"At the moment they (Team Sky) are really, really good. After the finish line, Wiggins made a gesture with his hand. He should not lack respect for his rivals," Nibali told reporters.
Nibali, winner of the Spanish Vuelta in 2010, lies two minutes 23 seconds behind Wiggins.
"I'm not saying he should just let me go but he should not show a lack of respect for his rivals because in cycling things change quickly," the Italian added.
"He is an exuberant rider but I'm not worried by it. After the finish line he stared at me and I really did not like that look.
"There has always been a lot of respect in cycling and this has to continue."