FBI Director James Comey said "no reasonable prosecutor" would pursue a case but said the likely Democratic presidential nominee was "extremely careless" with classified information.
The decision ends the legal uncertainty that has dogged the Clinton campaign.
However, Mr Comey was highly critical of Mrs Clinton and her staff.
"Although we did not find clear evidence that Secretary Clinton or her colleagues intended to violate laws governing the handling of classified information," Mr Comey said.
"There is evidence that they were extremely careless in their handling of very sensitive, highly classified information."
Analysis: Anthony Zurcher, BBC News North America Reporter
Although the criminal investigation into Hillary Clinton's private email server is drawing to a close, the political fallout could last through the November general election.
The top-line from James Comey's news conference - no recommended indictments - is positive for the presumptive Democratic nominee, but the bureau's findings are sure to sting.
At this point, Donald Trump and the Republicans have a choice. They could attack the FBI for failing to throw the book at Mrs Clinton - as many on the right will be up in arms over this. Or they could hammer the former secretary of state on what Comey did say - using his words to paint her as evasive and reckless.
Do the former, and their message will likely be written off as yet more partisan conspiracy-mongering. Do the latter, and the blows will likely land on target.
In the past Mr Trump has overplayed his hand when presented with a target of opportunity. He was widely criticised for his response to the Orlando attacks and the UK Brexit vote, for instance.
Now he has been handed a golden cudgel, courtesy of the FBI. Will he know how to use it?
The likely Democratic presidential nominee's use of private email has been a talking point in the election, with critics saying Mrs Clinton believes she is above the law.
Republican presidential hopeful Donald Trump called the decision "very unfair" and said Mrs Clinton's use of private email compromised national security.
The Clinton campaign said on Tuesday that they were "glad that this matter is now resolved".
Mrs Clinton said she set up the email address for reasons of convenience, because it was easier to do everything from one device than to have several phones or tablets.
The FBI's findings also contradicted some of Mrs Clinton's previous statements about her private email.
Mrs Clinton had previously said she did not knowingly send any classified material from her account.
However, the FBI found more than 100 emails that were classified at the time on Mrs Clinton's servers in multiple email chains.
The FBI ended its investigation after agents interviewed Mrs Clinton for more than three hours over the weekend about her email habits.
REUTERS
It is ultimately up to the Department of Justice to decide whether to press charges, but Attorney General Loretta Lynch has said she would be follow the FBI's recommendation.
Mrs Clinton's campaign says it showed that her practices were consistent with those of other secretaries of state who "also used personal email" and she was "not unique" in doing it.
However, Mrs Clinton has apologised for using the private email system, calling it "a mistake".
"As I look back at it now, even though it was allowed, I should have used two accounts. ... I'm sorry about that. I take responsibility," she said.
On Tuesday, Mrs Clinton and President Barack Obama will campaign together in North Carolina.
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