Ms Habba assailed the court's ruling as political, but said on X she was resigning "to protect the stability and integrity" of her office.
"But do not mistake compliance for surrender," she said, adding that the administration would continue its appeal of the court rulings ousting her from the position."
"This decision will not weaken the Justice Department and it will not weaken me."
Habba is one of several acting US attorneys around the country to have their appointments by the Trump administration challenged on the basis that they stayed in the temporary jobs longer than the law allows.
She said she would remain with the Justice Department as a senior adviser to US Attorney-General Pam Bondi.
Her former duties will, for now, be split between three Justice Department lawyers.
Habba, 41, was appointed in March to serve a temporary term as acting US attorney for New Jersey, a powerful post charged with enforcing federal criminal and civil law.
Once a partner in a small New Jersey law firm, Habba was among Mr Trump's most visible legal defenders before his return to the White House, representing him in court and frequently appearing on cable TV news on his behalf.
But she had a partisan bent and no experience as a prosecutor.
New Jersey's two Democratic senators indicated they would block her confirmation in the US Senate.
Asked about Habba's resignation on Monday, Trump lashed out at the Senate over its tradition of refusing to act on nominees if they are opposed by the senators representing the state involved.
"It's a horrible thing. It makes it impossible to appoint a judge or a US attorney," Mr Trump told reporters.
"I guess I just have to keep appointing people for three months and then just appoint another one, another one. It's a very sad situation. We're losing a lot of great people."
