FBI Director James Comey told Congress his agency’s review had found nothing to alter its original conclusion.
In July, he said Mrs Clinton had been careless but not criminal in handling sensitive material on her private email server while secretary of state.
The issue flared up again with the discovery of new “pertinent” emails.
They were reportedly found on the laptop of Anthony Weiner, the estranged husband of one of the Democratic presidential candidate’s closest advisers.
Mr Comey’s original letter late last month to lawmakers, revealing the bureau’s inquiry into Mrs Clinton’s emails had been revived, shook up the White House race and reinvigorated the campaign of Republican nominee Donald Trump.
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 almost certainly will continue to accuse his opponent of corruption and, perhaps, again allege the FBI is covering for her.
With only two days until 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.
The FBI director had announced that the agency would investigate if the newly discovered messages contained classified information.
But in Sunday’s follow-up, Mr Comey wrote: “Since my letter, the FBI investigative team has been working around the clock to process and review a large volume of emails from a device obtained in connection with an unrelated criminal investigation.
“During that process, we reviewed all of the communications that were to or from Hillary Clinton while she was Secretary of State.
“Based on our review, we have not changed our conclusions that we expressed in July with respect to Secretary Clinton.”
On board the candidate’s campaign airplane, her team said they were always confident of the outcome.
Communications director Jennifer Palmieri told media: “We’re glad this matter has been resolved.”
But the Trump team cried foul.
Newt Gingrich, an adviser to the Republican nominee, tweeted: “Comey must be under enormous political pressure to cave like this and announce something he cant [sic] possibly know.”
Trump campaign manager Kellyanne Conway tweeted: “If FBI conclusions remain unchanged, that means she still was reckless & careless, still lied about classified info, lied re: # of devices.”
Campaigning in Minnesota on Sunday, Mr Trump made no mention of Mr Comey’s findings.
But he did say Mrs Clinton “will be under investigation for a long, long time, likely concluding in a criminal trial”.
He also renewed his claims that the Democrat was being “protected by a rigged system”.
The FBI has already established Mrs Clinton had classified information on a private email server that was run out of her upstate New York home.
Mr Comey said in July that her handling of sensitive material during her 2009-13 tenure as secretary of state was “extremely careless”, but cleared her of criminal wrongdoing.
The revelation that she handled sensitive information while breaking federal rules by running her own email server has dogged her campaign since last year.
A new NBC/Wall St Journal opinion poll on Sunday before news broke of the FBI letter suggested a four-point lead for Mrs Clinton.
The latest Washington Post/ABC tracking poll put her lead at five points.
Sunday’s campaign stops take her to Ohio, Michigan, Pennsylvania and New Hampshire.
Also on Mr Trump’s itinerary were Iowa, Michigan, Pennsylvania and Virginia.