Rove, who masterminded president Bush's political campaigns in 2000 and 2004, has been under fire since 2003.
Witness to history
"I'm grateful to have been witness to history," an emotional Rove said on Monday as he appeared side by side with Bush and made his resignation official.
Rove said: "I've seen a man of farsighted courage put America on a war footing and protect us against a brutal enemy in a dangerous conflict that will shape this new century."
Bush praised him for making "enormous sacrifices" to serve, and in an acknowledgement of his own few days in power, said: "I will be on the road behind you here in a little bit."
Rove said: "I've asked a lot of my family, and they've given all I've asked and more.
"Now it seems the right time to start thinking about the next chapter in our family's life."
Tensions began when Joseph Wilson, a retired US diplomat, claimed Rove had illegally leaked to the media the identity of Wilson's wife, Valerie Plame, a covert employee of the CIA.
Wilson stated the leak had been planned in retaliation for his New York Times article, in which he refuted a claim by the Bush administration that the Iraqi government of Saddam Hussein had explored ways of purchasing uranium ore from Niger.
"Thank you Mr Bush. For showing the world that America can do anything it wants and get away with it"
hd3824, Akron, USA
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The claim, made by Bush in his 2003 State of the Union address, was widely used to justify the subsequent invasion of Iraq.
An investigation into the Plame leak led to perjury and obstruction of justice charges, and subsequent conviction of Lewis "Scooter" Libby, a former chief-of-staff for Richard Cheney, the vice-president.
But prosecutors determined last year there was no reason to charge Rove with any wrongdoing.
Asked in the Wall Street Journal interview if he felt he had committed any mistakes during his White House tenure, Rove said: "I'll put my feet up in September and think about that."