Valentina Matviyenko said in televised comments following Tuesday's signing that the 77-story glass-clad tower will be an "architectural masterpiece that future generations will be proud of."
Advocates say the building, called the Okhta Center, will be an important step in developing St. Petersburg. But critics denounce it as a crude show of political and commercial ego that spoils the unique spire-and-bridge cityscape.
"Today the governor has signed not a decree, but a verdict to herself for her reputation among the city residents," said Maxim Reznik, head of the St. Petersburg branch of the liberal Yabloko party.
Reznik said the decree was illegal. "I hope St. Petersburg residents have the strength to stand up to this," he said.
UNESCO has warned that building the 400-meter (1,300-foot) tower could endanger St. Petersburg's status as a world heritage site.
The decree was the final hurdle after city lawmakers approved the plan Sept. 22.
St. Petersburg has trailed far behind Moscow in cashing in on the country's post-Soviet economic transformation, and authorities see the tower as an important step in bringing the northern city into the high-tech business age.
Preservations reject the notion. A report last month from the Moscow Architecture Preservation Society called the St. Petersburg tower "the most monstrous project."
Some St. Petersburg residents have dubbed the design the "corn cob" or the "cigarette lighter" because of its shape.
The Okhta Center is to be built across the Neva river _ upriver from most of the city's tourist trails. It would still dominate many views and would loom over the Smolny monastery complex, whose turquoise buildings trimmed in frilly white are one of the city's most beloved sites.