They would remain on bases across the country, however, providing backup support to Iraqi forces until the end of 2011.
When finalised, the pact will still have to be ratified by the Iraqi parliament and the veto-wielding presidency council.
Al-Sadr and other critics fear that the pullout deal will bind the US and Iraq into a long-term security relationship, instead of restoring Iraqi sovereignty.
In Kufa, about 2,000 protesters marched after Friday prayers, chanting "No to America" and wielding portraits of al-Sadr and waving Iraqi flags.
Some held up banners reading "The dubious agreement means a permanent colonisation of Iraq" and "Iraq is not a US colony".
An aide to al-Sadr, Sheik Dia al-Shawki, told those gathered that the deal goes against the will of the Iraqi people.
In Baghdad's Sadr City district, supporters set fire to American flags while local leaders denounced an ambiguous agreement "that the Iraqi people know nothing about".
One of the most contentious issues of the security deal is Iraqi jurisdiction over US soldiers and military contractors, as the Iraqi forces assume greater responsibility.
The draft agreement says that private US contractors would be subject to Iraqi law - unlike at present. However, US troops would remain under US jurisdiction.
Mohammed Hamoud Bidan, Iraq's deputy foreign minister, on Friday told CNN that jurisdiction would be determined by a joint legal committee in cases of US citizens who commit major crimes against Iraqi civilians.
The deputy minister also repeated June 30 as the deadline for a US troop pullout from Iraqi cities.