Libby, 55, resigned and left the White House.
Karl Rove, Mr. Bush's closest adviser, escaped indictment Friday but remained under investigation, his legal status shadowing a White House already in trouble. The U.S. military death toll in Iraq exceeded 2,000 this week, and the president's approval ratings are at the lowest point since he took office in 2001.
In brief remarks outside the White House, Mr. Bush called the legal proceedings "serious" and said he was "saddened" by the indictment and resignation of Libby.
But he said he still has "a job to do," and so do the people who work with him.
Mr. Bush praised Libby's service and said he is "presumed innocent and entitled to due process."
Friday's charges stemmed from a two-year investigation by special counsel into whether Rove, Libby or any other administration officials knowingly revealed the identity of CIA officer Valerie Plame or misled investigators about their involvement.
In the end, Fitzgerald accused Libby of a cover-up — lying about his conversations with reporters. He was not charged with outing a spy.
"Mr. Libby's story that he was at the tail end of a chain of phone calls, passing on from one reporter what he heard from another, was not true. It was false," the prosecutor said. "He was at the beginning of the chain of the phone calls, the first official to disclose this information outside the government to a reporter. And he lied about it afterward, under oath, repeatedly."
the Special Counsel's statement (.pdf).
Libby's indictment is a political embarrassment for the president, paving the way for a possible trial renewing the focus on the administration's faulty rationale for going to war against Iraq — the erroneous assertion that Saddam Hussein possessed weapons of mass destruction.
CBS News legal analyst Andrew Cohen reports the indictment "makes it very likely, almost a certainty" that Vice President Dick Cheney will have to testify in the criminal trial against Libby.
If so, Cheney, who prizes secrecy, will be called upon as a witness to explain why the administration launched a campaign against Plame's husband, diplomat Joseph Wilson, a critic of the war who questioned Mr. Bush's assertion that Iraq had sought nuclear material.
The indictment said the vice president advised Libby that Wilson's wife worked at the CIA but the vice president was not the first administration official to tell him about it.
At a news conference, Fitzgerald said the inquiry was substantially complete, though he added ominously, "It's not over." He declined to comment about Rove's involvement. Asked about Cheney, he said: "I'm not making allegations about anyone not charged in the indictment."
The grand jury indictment charged Libby with one count of obstruction of justice, two of perjury and two of making false statements. If convicted on all five, he could face as much as 30 years in prison and $1.25 million in fines.
Democrats suggested the indictment was just the tip of the iceberg. Senate Minority Leader Harry Reid, D-Nev., said the case was "about how the Bush White House manufactured and manipulated intelligence in order to bolster its case for the war in Iraq and to discredit anyone who dared to challenge the president."
Cheney and several other officials were mentioned by title in the 22-page indictment, but no one besides Libby was charged.