The Board of Supervisors on Tuesday night approved the sprawling 5M project at Fifth and Mission, a $1 billion development that could become a South of Market game-changer as formative as the creation of Yerba Buena Gardens or Moscone Center.

For several hours, opponents of the project paraded to the lectern to plead with the supervisors to uphold an appeal of the environmental impact report on the development, which they argued would send land prices skyrocketing, prompt landlords to jack up rents, and squeeze out the working-class and elderly Filipino residents who have managed to hang on over the last 15 years amid waves of South of Market gentrification.

But in the end, the supervisors concluded that the project’s benefits — 40 percent low-income and middle class housing, open space, and money for local institutions like the Bessie Carmichael School and the Gene Friend Recreation Center — outweighed any gentrifying effects the development will have on the area.

The votes to affirm the project were 8-3, with Supervisors John Avalos, Eric Mar and David Campos voting against it.

Gabriel Metcalf, executive director of the urban think tank SPUR — located 2 1/2 blocks east the project — said the debate over 5M was less about the project and more about broader housing policy.

“There is not a disagreement on any side that there is a crisis of displacement in the city,” Metcalf told the supervisors as he spoke in support of 5M. “I know these votes are never very easy, but you will almost never get a project this good before you again.”

The vote came a week after the developers, Forest City Enterprises and the Hearst Corp., which owns The Chronicle, entered into an agreement with Supervisor Jane Kim to increase the number of affordable housing while cutting the number of parking spaces.

The development agreement, hammered out by Kim and Forest City Senior Vice President Alexa Arena, calls for 87 affordable apartments in a 288-unit rental building, up from the previous proposal of 58. The additional units will target households earning 150 percent of area median income, about $150,000 for a family of four.

Parking spaces reduced

The amount of parking will be reduced from 463 to 331 spaces. The project will also fund an 83-unit, 100 percent affordable senior project just to the west of the 5M parcel and a 103-unit family development at Eddy and Taylor streets.

The project includes a 614,000-square-foot office complex at Fifth and Howard streets, a 400-unit, 470-foot-tall condominium tower at Fifth and Minna streets, and the rental apartment building on Mission Street between Fifth and Sixth streets. Construction is expected to begin in about a year.

Some speakers at the supervisors meeting took issue with the decision to use some of the subsidized housing to meet the needs of middle class residents earning $150,000 for a household of four. Teacher Valerie Fernandez said that the upper level area median income threshold leaves out a lot of young teachers who earn significantly less than $75,000.

“I won’t qualify for 10 years,” she said. “Is it fair to be asked to wait another decade to be able to live in the same community I teach in? I do not want to be the teacher who has to commute on BART and not even know what happened in San Francisco the night before.”

But Michael Theriault, secretary-treasurer of the San Francisco Building Trades Council, said middle income housing is well-suited to the income levels of tens of thousands of people who can’t afford to stay in the city, including members of his union.

“We are in that economic class that for a generation has been least well-served by affordable housing politics,” he said. “We make too little to afford market rate, except in a few outlying neighborhoods, and we make too much to qualify for subsidized housing.”

Avalos’ thinking

Supervisor John Avalos, who voted against upholding the environmental impact report, said he felt more comfortable standing with the grassroots groups fighting displacement.

“It’s not about tearing down buildings, it’s about rezoning an area and what the impact that is going to be on the people already there,” Avalos said. “I want to stand on the right side of history.”

There are about 8,000 housing units within one-quarter mile of 5M, 90 percent protected because they are low-income housing run by nonprofits, single room occupancy hotels or older, rent controlled buildings.

Kim, who faced criticism from Filipino nonprofit groups in her district that typically support her, ticked off a long list of community benefits from the project, including $800,000 going the establishment of a Filipino Cultural Heritage District, $1.5 million for the Gene Friend Rec Center and $1 million for Victoria Manalo Draves Park.

She also pointed out that taken together, all of the affordable units in the three buildings have an average area median income weight of 75 percent, about $76,000 for a family of four. The average AMI weight of a similar deal the San Francisco Giants are building in Mission Bay is closer to 100 percent, $101,000 for a family of four.

“If we can’t support a project at 40 percent (affordable housing), I’m not sure what kind of project this board can support,” said Kim. “It’s not just about building as many market rate units has I can, it’s about balance.”

“This milestone represents the start of our continued work with the community to ensure that the approved project is the best it can be over the long-term,” Arena said.