A pardon was announced for rapper Lil Wayne and commutations for rapper Kodak Black and former Detroit Mayor Kwame Kilpatrick.
In a farewell video message on Tuesday, Mr Trump called on Americans to pray for the incoming administration, though he did not mention his successor by name.
He said he was proud of what he had achieved over the past four years, highlighting his Middle East peace deals and his record as the first president in decades not to start any wars.
But the political drama surrounding him is far from over. The US Senate is expected to put him on trial soon, following his record second impeachment by the House of Representatives for allegedly inciting the Capitol riot.
On Tuesday, the Senate's Republican leader, Mitch McConnell, said the mob had been provoked by Mr Trump and fed lies.
What did Biden do on the eve of inauguration?
Mr Biden had planned to take an Amtrak train into Washington, as he did so often during his years as a veteran senator.
But amid all the heightened security, he instead opted to fly in a private plane to Joint Base Andrews.
On Tuesday evening, he and Ms Harris led a tribute at the reflecting pool in front of the Lincoln Memorial to the 400,000 Americans lost to Covid-19.
They were almost alone on the National Mall, where some 200,000 flags have been planted to represent the crowds who will be absent at Wednesday's inauguration.
Earlier on Tuesday, Mr Biden wept as he prepared to embark from his hometown of Wilmington, Delaware.
"These are dark times," he told dozens of supporters. "But there's always light."
Mr Biden stayed on Tuesday night with his wife Jill in Blair House, a residence for heads of state and other important visitors across the road from the White House.
What will Biden do on his first day?
Mr Biden plans to issue a flurry of executive orders.
Among other measures, he is expected to reverse Mr Trump's withdrawal of the US from the Paris climate accord, cancel his predecessor's travel ban on visitors from several mainly Muslim countries, and unveil a bill to provide an eight-year path to citizenship for an estimated 11 million undocumented immigrants living in the US.
What will Joe Biden do first?
Does Biden's new team better reflect America?
His vice-president will swear in three new Democratic senators on Wednesday, leaving the upper chamber of Congress evenly split between the two main parties, and allowing Ms Harris to cast the deciding vote on any deadlocked legislation.
Mr Biden's legislative ambitions could be tempered by the slender majorities he holds in both the Senate and House of Representatives.
Five of his Cabinet picks - Antony Blinken (state department), Janet Yellen (Treasury), Lloyd Austin (Pentagon), Alejandro Mayorkas (Homeland Security) and Avril Haines (Director of National Intelligence) - are undergoing confirmation hearings before Senate committees.
What's the mood like in Washington?
Some 25,000 National Guard troops are guarding the Capitol, White House and National Mall, which are also protected by a ring of steel made up of barricades and tall fencing.
Largely emptied of ordinary Americans, central Washington DC has been carved up into "green" and "red" zones reminiscent of war-torn Baghdad.
Ahead of Mr Biden's arrival in the city, 12 National Guard members were removed from the presidential inauguration security mission after they were found to have ties with right-wing militia groups or posted extremist views online.
There was no threat to Mr Biden, officials said.