The Republican nominee cried foul after learning about the law enforcement bureau's decision.
At a rally in the Detroit suburbs, Mr Trump insisted it would have been impossible for the FBI to review what has been reported to be as many as 650,000 emails in such a short time.
"Right now she's being protected by a rigged system. It's a totally rigged system. I've been saying it for a long time," he told supporters in Sterling Heights, Michigan.
"Hillary Clinton is guilty, she knows it, the FBI knows it, the people know it and now it's up to the American people to deliver justice at the ballot box on November 8."
While Mrs Clinton herself did not address the FBI director's letter on the trail, her campaign said it was always confident she would be cleared.
In Manchester, New Hampshire, on Sunday, she said the country was facing "a moment of reckoning" and Americans must choose between "division and unity".
In July, the FBI said she had been "extremely careless" to handle classified material on a private email server as secretary of state from 2009-13, but it had found no evidence she committed a crime.
However, 11 days before the election, FBI director James Comey had pitched the race into turmoil by announcing a newly discovered batch of Clinton emails would be investigated.
The bombshell infuriated the Clinton camp, but threw a lifeline to a Trump campaign that had been receding in the polls.
Analysis - Anthony Zurcher, BBC News, Washington
It was much ado about nothing, but it certainly amounted to something. While FBI Director James Comey, in effect, said "never mind" with regards to Hillary Clinton's emails, for the past two weeks the story has dominated the political conversation, and Democrats have paid a price.
While Mrs Clinton's presidential hopes have stabilised, talk of a possible rout - and sweeping down-ballot victories in congressional races - are a distant memory.
Mrs Clinton will now try to focus on her closing campaign message. Donald Trump will continue to accuse his opponent of corruption and, perhaps, again allege the FBI is covering for her.
On the eve of voting, the dust kicked up by this story won't have fully settled by the time Americans head to the polls.
Once this election is over, there should be serious soul-searching within the FBI and the media about how this saga played out. The nation's top law-enforcement agency was a source of constant leaks, as internal disputes spilled into public view.
If Mr Trump wins, many on the left will blame Mr Comey for the result. If Mrs Clinton prevails, she likely will bear a lasting grudge over this political near-miss.
In a letter to Congress on Sunday, Mr Comey said his investigators had "worked around the clock" on the latest emails, which were found in early October in a separate investigation.
The messages reportedly turned up on a laptop belonging to the estranged husband of one of Mrs Clinton's closest advisers, former congressman Anthony Weiner, who is accused of sending illicit messages to a 15-year-old girl.
Mr Comey said investigators had found no reason to change the FBI's earlier assessment that Mrs Clinton should not be charged for her handing of classified information.
Both candidates are set for a whistle-stop tour of battleground states on Monday, in a last-ditch dash for votes.
Mrs Clinton starts the day in Michigan, a traditional Rust Belt, Democratic stronghold that has been heavily targeted by Mr Trump in recent days.
She will then head to Philadelphia where she will be joined by President Barack Obama, First Lady Michelle Obama, husband Bill Clinton and Bruce Springsteen.
The Democratic candidate will end her White House campaign with a midnight "get out the vote rally" in North Carolina.
Mr Trump heads to Florida, North Carolina and Philadelphia before ending with a rally in Grand Rapids, Michigan.
In states where early voting is allowed, nearly 42 million Americans have already cast ballots in the presidential election.
They have turned out in record numbers in crucial battlegrounds such as Florida, North Carolina and Nevada.
An estimated 126 million voters cast ballots in the 2012 White House election.