The moves may spearhead the swift removal of other such memorials in the city. Mayor Bill de Blasio tweeted Wednesday afternoon that the city will conduct a 90-day review of “all symbols of hate on city property,” adding that a plaque honoring former Nazi collaborator Philippe Pétain found in the Canyon of Heroes “will be one of the first we remove.”

Gov. Andrew M. Cuomo also sent a letter to the Army urging it to reconsider its rejection of a request to rename General Lee Avenue and Stonewall Jackson Way in Fort Hamilton.

The Bay Ridge church’s plaques, which were erected by the United Daughters of the Confederacy in 1912 and 1935, were the subject of a New Yorker article in June and had come under increased scrutiny in recent days following the violent white supremacist protests against the proposal to remove the Robert E. Lee statue in Charlottesville.

The church, which was known as the “Church of the Generals,” was closed in 2014.

Provenzano said he ordered the plaques to be taken down as soon as he became aware of them over the weekend. Crews spent less than five minutes removing the plaques with electric saws to the cheers of a few onlookers Wednesday morning.

“I’m glad it’s gone,” said Bay Ridge resident Emily Hegarty, who attended the church and is an English professor. “We thought it was anachronistic. . . . The Daughters of the Confederacy had their own agenda.”

There were, however, a few Bay Ridge residents who questioned the removal.

Patrick Gilbride, who has lived in the neighborhood since 2001, said the plaques served as a symbol of reconciliation.

“It might be educational to say, ‘This is an olive branch,’ ” he said.

Hegerty countered that such a public display of a racist past didn’t belong in a diverse neighborhood.

“They didn’t go to this church. They are here to make a political point,” she said of those opposing the removal.

The plaques will be placed in the diocese’s archives in Garden City and be made available to view by request, Provenzano said.

“It will be put in a place where it will be remembered in terms of its history and the proper sense of how it is viewed,” he said.

The Bronx Community College’s 630-foot Hall of Great Americans, which opened in 1900, has also been put under scrutiny. The busts of Lee and Jackson were installed between 1901 and 1973 when the school was part of NYU and honorees were decided by votes from the public.

The school is committed to addressing concerns around the controversial figures in the hall, Karla Renee Williams, the college’s legal counsel, said.

“The national movement is a reflection of what society is feeling right now,” she said.

Mark Naison, professor of history and African-American studies at Fordham University, predicted the efforts to remove Confederate memorials from New York spaces will be swift and gain support fast.

“There’s a lot of momentum to this, and it’s not going away,” he said.