Council members representing the district agreed to the rezoning after working out a compromise to increase the amount of affordable housing. The vote passed 47-2 during a heated meeting.
But some residents remained opposed, saying it would destroy the neighborhood's cultural history and price out longtime, lower-income residents and obstruct pedestrians' views of the sky.
Before the vote, the balcony at City Hall was cleared because Harlem residents opposed to the rezoning booed supporters as they spoke.
"But they didn't clear (the balcony) when they were cheering" for the plan, said Councilman Charles Barron, who voted against the rezoning plan. The approval, he said, "continues the gentrification of Harlem."
"The development should be from the bottom up, from the people up, not from the top down, from rich white developers and the city planning commission," Barron said after the vote. "Ten to 12 years from now, they will see that the housing will not be affordable. This will be the wholesale sellout of Harlem from river to river."
The city Planning Commission approved the plan in March.
Queens Councilman Tony Avella, who cast the other opposition vote, has said the rezoning would "push out" longtime small businesses and that the real estate industry lobbied for the rezoning changes.
Councilwoman Inez E. Dickens, whose district includes the rezoned area and who was born and raised in the neighborhood, insisted Wednesday that Harlem's historic and cultural character would be protected.
"My priority was to make sure that those who had laid down roots in Harlem both in business and as long time Harlem residents and who had stayed in Harlem in good times and bad would not be displaced," Dickens said in a statement. "I am most pleased that we were able to create an unprecedented amount of affordable and income-targeted housing opportunities."
The city has promised to provide help to local businesses, improvements to Marcus Garvey Park, address health problems among residents, and make sure that 46 percent of all new housing units in the rezoned and surrounding areas on city-owned property is income-targeted.
Mayor Michael Bloomberg said the council's approval will "strengthen" the area's business district and "bolster" arts, entertainment and retail there. The rezoning also will create more than 7,000 jobs, he said.
"Not only does the plan lay the foundation for economic growth on Harlem's Main Street, but also it preserves its noted brownstones and reinforces its arts and culture heritage," Bloomberg said in a statement.
Harlem includes such landmarks as the Apollo Theater and Hotel Theresa, where Louis Armstrong, Lena Horne and Fidel Castro stayed and where Malcolm X held meetings of the Organization of Afro-American Unity after breaking from the Nation of Islam.
The Apollo Theater Foundation has expressed support for the rezoning.