President Bush's top political adviser Karl Rove was not indicted, but reportedly remained under investigation.
At a news conference, Fitzgerald said the inquiry was substantially complete, but added, "It's not over."
The charges are the first in a two-year investigation prompted by the public disclosure of CIA operative Valerie Plame's identity in a July 14, 2003 newspaper column by Robert Novak.
Plame's name was leaked to the media after her husband, former Ambassador Joseph Wilson, challenged President Bush's claim in his State of the Union address that Iraq had tried to buy uranium from the African nation of Niger.
When making the case to go to war with Iraq in 2003, President Bush had said former Iraqi dictator Saddam Hussein's weapons of mass destruction program posed an immediate threat to the United States.
Libby, 55, is considered a chief architect of the war with Iraq and analysts say a trial would provide a glimpse into how President Bush and his team built the case to go to war.
The five-count indictment accuses Libby of lying about how and when he learned about Plame's identity in 2003 and then told reporters about it, according to the Associated Press.
The indictment says Libby engaged in obstruction of justice by impeding Fitzgerald's investigation.
The charges are all felonies.
Libby reportedly submitted his resignation to White House chief of staff Andy Card. It was accepted and Libby left the White House.