Opera Plaza Cinema, the struggling Civic Center movie house that had been scheduled to shut down, has a new nonprofit owner and a fresh long-term lease.

The San Francisco Neighborhood Theater Foundation is taking over the four-screen cinema, which has long specialized in independent movies rarely shown shown at San Francisco megaplexes. The foundation will invest $1.2 million into updating the space, according to board members Jack Bair and Alfonso Felder, San Francisco Giants executives who co-founded the foundation in 2002.

Opera Plaza Cinema is the third theater the foundation has taken over. It owns the Vogue Theater on Sacramento Street and leases the Balboa Theater in the Richmond District.

The foundation signed a 10-year lease for Opera Plaza Cinema with the landlord, Pacific Union Development Co. Longtime operator Landmark Theaters will continue to run the theater.

The deal comes more than two years after the property owner determined that the cinema was “no longer economically viable” and submitted an application to convert the theater into office space. For years the property owner had been subsidizing Landmark’s operations.

The news of the theater’s demise caught the attention of the foundation, as well as a group of philanthropic cinephiles who agreed to contribute the $1.2 million to save the theater. Venture capitalist Arthur Rock, apartment building owner Russell Flynn, First Republic Bank CEO Jim Herbert and wife Cecilia Herbert, board chair of Blackrock’s iShares Exchange Traded Funds, were the donors.

“We just love movies and we appreciate having the ability to see a wide variety of films, not just blockbusters,” Cecilia Herbert said. “The lovely thing about the programming at Opera Plaza is it’s been interesting small movies rather the giant ones with $200 million budgets. We have seen many small, thoughtful movies there.”

Felder and Bair said new seating, concessions and screens, and a revamped layout would make Opera Plaza Cinema competitive with newer theaters around the city. At least part of the theater will remain open while it’s renovated.

“The seats, the screens, the overall experience is something that needs an upgrade,” Felder said. “The theater has fallen behind.”

The news comes as Van Ness Avenue has struggled with retail vacancies, caused both by the migration to online shopping and years of construction of the long-delayed $316 million Bus Rapid Transit line, which is expected to open next year.

The AMC 14 Theater at 1000 Van Ness Ave. and a CVS pharmacy at Sutter Street and Van Ness Avenue shut down last year, and the former Circuit City at 1200 Van Ness Ave. has been empty for years. A South Korean theater chain known for futuristic “4D” auditoriums, has plans to take over the former AMC 14, pulling permits in October to renovate the multiplex theater, according to building department records.

Nathan Nishiguchi of Urban Pacific Properties, which built the 462-unit Opera Plaza condo complex and owns 100,000 square feet of commercial space there, said his group had been subsidizing the theater for years. While Union Pacific didn’t want to lose the theater, the company wasn’t in a position to invest in the capital improvements needed to keep it competitive, he said.

Nishiguchi said all of Opera Plaza’s retail tenants have suffered from the bus rapid transit construction, especially bookstore Books Inc. and Max’s Opera Cafe, a restaurant that has been a popular pre-show dining spot for theater and opera patrons.

“We are hoping that having the foundation reinvigorate the theater will bring more foot traffic to the plaza and help all of our small businesses,” Nishiguchi said.

Andy Perham, CEO of Books Inc., said that he is “thrilled the movie theater is staying here.”

“The last couple of years with Van Ness torn up has been a real frustration,” he said. “There was heavy machinery just living in front of our store for a year. It would have been hard to hide us more effectively.”

Marlayne Morgan, of the Cathedral Hill Neighborhood Association, said Opera Plaza has been “a big part of the performing arts district,” which includes SFJazz, the San Francisco Symphony, the San Francisco Opera and the Sydney Goldstein Theater.

“Opera Plaza is the only theater in the district that focuses on film,” she said. “I think Van Ness is going to get a shot in the arm when BRT opens, and we would like to see the performing arts district expand up Van Ness.”

When it opened in 1980, Opera Plaza was an pioneer in a new generation of transit-oriented urban development. But the design of the complex — set far back from the sidewalk with a spacious courtyard and fountain separating the retail from foot traffic — makes it hard to find.

The plan is to install more visible signage, which will help introduce the theater to new residents who have moved into the more than 4,000 housing units added over the past decade in the greater Civic Center neighborhoods, including Upper Market, Hayes Valley, Mid-Market and Lower Polk Street.

“There is a whole neighborhood that has grown up around the theater and needs to be reintroduced to it,” Bair said. “A lot of newcomers don’t know it’s here.”

Meanwhile, the foundation is in talks to save another neighborhood theater: the Clay Theater in Pacific Heights, which ceased operations this month. Jim Herbert said his group is hoping to “help restore and preserve this cultural treasure for the benefit of future generations.”

J.K. Dineen is a San Francisco Chronicle staff writer. Email: jdineen@sfchronicle.com Twitter: @sfjkdineen