"I did not resign. Moments ago I was fired. Being the US Attorney in SDNY will forever be the greatest honour of my professional life," Mr Bharara tweeted from his personal verified Twitter account, making a reference to his jurisdiction the Southern District of New York.
Mr Bharara, 48, one of the most high-profile federal prosecutors in the US known for crusading against public corruption, had been asked by the acting deputy attorney general yesterday to immediately submit resignations.
Earlier, sources close to Mr Bharara had said that the Manhattan federal prosecutor had refused to submit his resignation, in effect preparing for a show down with President Donald Trump.
The order by acting deputy attorney general Dana Boente asking the 46 remaining federal attorneys to resign was met with shock by Mr Bharara's office since US President Trump had last year in November asked him to stay on in his administration.
Mr Bharara had met President Trump in the Trump Towers in Manhattan shortly after the Republican nominee had won the presidential elections. Talking to reporters following his meeting with President Trump, Mr Bharara had said he was asked by President Trump to remain in his current post at the meeting and had agreed to do so.
CNN quoted a statement Saturday from Senator Chuck Schumer saying he was "troubled" to learn of the Trump administration's request for Mr Bharara's and other US attorneys' resignations, adding that the President initiated a call to him in November "and assured me he wanted Mr Bharara to continue to serve as US Attorney for the Southern District.
"While it's true that presidents from both parties made their own choices for US attorney positions across the country, they have always done so in an orderly fashion that doesn't put ongoing investigations at risk," the New York Democrat said. "They ask for letters of resignation, but the attorneys are allowed to stay on the job until their successor is confirmed."
Mr Bharara has made a national and international mark for himself with many high-profile cases and investigations including foreign countries, insider trading and those involving US politicians. It was under his prosecution that India-born former Goldman Sachs director Rajat Gupta was convicted for insider trading in 2012.
Mr Bharara has served 7 years as the US attorney for the Southern District of New York, a jurisdiction that includes Trump Tower.