The protesters urged Russian President Dmitry Medvedev to ban the construction of the 77-story glass tower in the historic city center.
Officials see the so-called Okhta Center as an important step in developing St. Petersburg. But critics say the 400-meter (1,300-foot) tower will spoil the city's elegant skyline, known for its canals, ridges and centuries-old palaces. UNESCO has warned that building the tower could endanger St. Petersburg's status as a world heritage site.
The protesters on Saturday carried placards saying "No to the Tower!" and "History is More Important Than Money!"
They also called on Medvedev to fire city Gov. Valentina Matviyenko for giving a green light to the project earlier this month.
"This action will destroy my city, the city where I grew up, and the city that I want to save for my grandchildren," Galina Safronova, a 55-year protester said.
The proposed tower would be built across the Neva and upriver from the most heavily visited parts of St. Petersburg, but 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.
Russia's Culture Minister Alexander Avdeyev has joined the ranks of the project's foes. In an interview published Saturday in the business daily Kommersant, he said he had sent a letter to prosecutors arguing that the plan would violate the federal law.
"If the law is broken, the executive authorities and the prosecutors must react to that," Avdeyev was quoted as saying.
A poll of 1,200 St. Petersburg residents conducted earlier this week had 77 percent of respondents saying that the city's skyline must be preserved, while 18 percent welcomed new tall buildings and the rest were undecided. A margin of error for the poll conducted by the respected All-Russia Opinion Research Center wasn't given, but it usually is about 3 percentage points.