The U.S. military was required to pull back combat troops from cities by Tuesday as part of a security pact that calls for a full withdrawal of American forces by the end of 2011.
But some 130,000 U.S. troops remain in Iraq and the military says a small number of them will stay in cities as trainers and advisers at the request of the Iraqi government.
The military also has said it will continue to provide intelligence, air power, medical and logistical assistance to Iraq's fledgling, 650,000-member security force. U.S. troops will go back into cities on missions only if requested by the Iraqis.
The anti-U.S. cleric sought to cast the move as a victory for those who have opposed the American presence in Iraq.
"If it is a real withdrawal, then it is a medal of honor and a bright page in the history of honest Iraqi resistance that has been giving everything for the sake of liberating and serving its people and land," he said in a statement posted on his Web page.
But al-Sadr, who is believed to be in Iran, said the decision to keep some U.S. troops in cities shows the government and the U.S. "are not serious" about the timelines.
"If the occupation forces breach the claimed withdrawal even with the government's cover, then the people have the right to express their opinion by peaceful means and the right of self-defense in a way that does not harm the Iraqi people or security forces," he added.
Al-Sadr's militiamen fought fierce battles with U.S. forces in 2004 and were believed responsible for brutal retaliatory sectarian attacks against Sunnis. But the cleric called a cease-fire after U.S.-backed government offensives routed his fighters.
The statement came as the Iraqi government continued to celebrate the U.S. withdrawal with a military parade in the northern city of Mosul, which continues to be a hotbed of insurgent activity.
Violence has declined sharply in Iraq, but a series of deadly bombings in the days surrounding the withdrawal deadline have raised concerns about the readiness of Iraqi forces to take over their own security.
The latest was a car bombing of a market Tuesday in the ethnically tense northern city of Kirkuk that killed at least 33 people.
President Jalal Talabani, a Kurd, vowed the violence would not derail the security gains of the past two years.
"This terrorist attack will not deter Iraqis from continuing to combat terrorists," he said.
The bombing marred what otherwise was a festive occasion as Iraqis commemorated the newly declared National Sovereignty Day with military parades and marching bands in the capital.
The stakes are high. Failure by Iraqi security forces could plunge the country into a new round of sectarian warfare. Success would allow reconstruction projects to go ahead and give leaders of Iraq's rival ethnic and religious groups space to negotiate an enduring power-sharing formula.
Echoing U.S. and Iraqi military leaders, President Barack Obama predicted new flare-ups of violence.
"Make no mistake," Obama said Tuesday in Washington, "there will be difficult days ahead."
U.S. military officials have been purposely vague about the size and composition of the U.S. force that will stay on in urban areas. Publicizing a number, no matter how small, could irritate some Iraqis for whom the U.S. pullback is a proud moment of national significance. And if those troops' job description sounds too much like current combat operations, it could undermine the U.S. rationale for the withdrawal.
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