Donald Trump’s name has been removed from the facade of the Kennedy Center in Washington DC, hours after a judge rejected an emergency appeal to block the removal of the president’s name.

Work began in the early hours of Saturday, shortly after the performing arts venue missed a federal judge’s two-week deadline to excise the words “The Donald J Trump and” from its exterior by Friday at 11.59pm local time.

The extra words were added last December after Trump’s handpicked board of trustees voted unanimously to rename the venue, which was designated as a living memorial to the 35th US president, John F Kennedy, by Congress in 1964 and opened in 1971.

After erecting scaffolding on Friday evening, workers in hard hats and hi-vis vests draped tarpaulin over the temporary structure at 2am to block public views of their progress but were seen, through a small opening in the scaffolding covering, to be removing the letters at about 3am.

The tarpaulin remained in place on Saturday, but in a legal filing the executive director of the Kennedy Center confirmed the lettering had been removed.

Matt Floca, who is also the center’s chief operating officer, told the court that he was a “responsible official of the Kennedy Center” qualified to certify compliance with the order.

He wrote that the board of trustees and the center had removed “all physical signage on the Kennedy Center building and grounds, including the front portico, that purports to rename the Kennedy Center after President Trump”.

A crowd gathered in the front of the centre overnight to cheer on the workers and witness the moment the words would be restored to “The John F Kennedy Memorial Center for the Performing Arts”. People chanted “Shame!” and “Take it down!”.

It took about 30 minutes for Trump’s name to be removed.

The US district judge Christopher Cooper ruled last month that Trump’s name had been illegally added and ordered its removal this week, after a legal challenge brought by Joyce Beatty, a Democratic representative of Ohio, who is an ex-officio member of the Kennedy Center’s board.

“Congress gave the Kennedy Center its name,” the judge wrote in his 94-page opinion, “and only Congress can change it.”

Cooper also issued a temporary block on Trump’s demand to close the Kennedy Center for two years of renovations, which was due to start in July.

Trump reacted by saying he was giving up control of the venue, which he seized in February by removing the 18 trustees appointed to its board by the former president Joe Biden, handpicking new ones and naming himself chair.

Yet less than 36 hours before the deadline, lawyers acting for Trump and the Kennedy Center board mounted a last-minute attempt to keep his name on the building.

By then, the venue had already removed Trump’s name from its website and had reportedly sent out emails offering tickets to an event at “the Kennedy Center” – without including the 47th president’s name.

At 1pm on Friday, Cooper ruled that the centre’s lawyers had failed to demonstrate they were likely to win their appeal or that the centre would suffer “irreparable harm” if Trump’s name were purged.

Lawyers for the Department of Justice, representing the centre, then appealed Cooper’s denial at 3.46pm. In urging the appeals court to pause the order, the justice department said: “It does not make sense to alter the centre’s name and signage now, only to potentially revert the name again after what should be a successful appeal.”

But shortly after 7pm, this second attempt was denied, causing the crowd of more than 100 people at the Hands Off the Arts rally in front of the centre to erupt in cheers and demand the immediate removal of Trump’s name.

Late on Friday, the Department of Justice said in a court filing it would miss the deadline because of thunderstorms that could pose safety risks for the workers, seeking a 12-hour extension. Beatty called that request “inexcusable” and part of “a pattern of non-compliance”, according to the justice department filing.

During his second term, Trump has made a broad push to reshape areas of Washington. He has released plans ​for a 250ft arch near the Arlington national cemetery, and a 90,000-sq-ft ballroom is under construction on the former site of the East Wing of the White House, which Trump had demolished in October.

A court blocked construction of the $400m ballroom earlier this month; the Trump administration has appealed the decision.