Tolokonsky, who was nominated by President Vladimir Putin and introduced by the presidential envoy to the Siberian Federal District, was approved with 74 votes for and three against.
During his speech in the local legislature, he said the Novosibirsk Region, which currently enjoys a 9% industrial and 13% overall growth, is in line to become Russia's most developed region.
He also said the region's GDP is expected to double by the end of the year.
Tolokonsky was elected Novosibirsk mayor in March 1996. Since January 2000, Tolokonsky has held the post of the region's governor.