The pardon also covers all politicians who served on the congressional select committee that investigated the January 6, 2021 storming of the Capitol by Trump supporters, and police officers who testified before it.
Tump, who will return to the presidency later on Monday, has called for the punishment of his perceived enemies since winning the White House in November.
Biden praised public servants as the "lifeblood of our democracy."
Without mentioning Trump, he expressed alarm in a statement that some of them were subjected to threats and intimidation for doing their job.
"These public servants have served our nation with honour and distinction and do not deserve to be the targets of unjustified and politically motivated prosecutions," Biden said.
"Rather than accept accountability, those who perpetrated the January 6th attack have taken every opportunity to undermine and intimidate those who participated in the Select Committee in an attempt to rewrite history, erase the stain of January 6th for partisan gain and seek revenge, including by threatening criminal prosecutions," Biden said.
Trump in December backed a call for the FBI to investigate fellow Republican Liz Cheney over her role in leading Congress' probe of the January 6, 2021 riots at the US Capitol.
Fauci often clashed with Trump during the COVID-19 pandemic and his supporters and libertarians have continued to criticise the former senior health official, who they blame for mask mandates and other policies they believe infringed on people's rights.
Milley was quoted in the book War by Bob Woodward, which was published last month, calling Trump "fascist to the core".
Anthony Fauci advised on policies regarding the COVID-19 pandemic during Donald Trump's presidency. (AP PHOTO)
It is customary for a president to grant clemency at the end of his term but those acts of mercy are usually offered to everyday citizens who have been convicted of crimes.
But Biden has used the power in the broadest and most untested way possible: to pardon those who have not even been investigated yet.
And with the acceptance comes a tacit admission of guilt or wrongdoing, even though those who have been pardoned have not been formally accused of any crimes.
The decision lays the groundwork for an even more expansive use of pardons by Trump and future presidents.
It is unclear whether those pardoned by Biden would need to apply for the clemency or even accept the offer at all.
Any acceptance could be seen as a tacit admission of guilt or wrongdoing even though those who have been pardoned have not been formally accused of any crimes.
"These are exceptional circumstances, and I cannot in good conscience do nothing," Biden said, adding that "Even when individuals have done nothing wrong - and in fact have done the right thing - and will ultimately be exonerated, the mere fact of being investigated or prosecuted can irreparably damage reputations and finances."
with AP
