Bassim Fayadh, head of the political bureau of the Sayyid al-Shuhuda, said: "Today the Iraqi people, and more specifically, the people of Basra, have took to the streets to express their utter rejection of any agreement, which infringes on Iraq's sovereignty.
"We pin hopes on the Iraqi government and the legislative authority to protect Iraq's unity through the negotiation of this agreement and approval on condition that it does not violate Iraq's sovereignty," he said.
Previous protests against the deal have been lead by supporters of Muqtada al-Sadr, a Shia leader who has rejected any agreement with US forces.
But the Supreme Islamic Iraqi Council is apprently still deciding whether to support the so-called Status of Forces Agreement (Sofa), and its decision could be crucial in determining whether any deal passes the 275-member parliament.
On Tuesday, Iraq's cabinet said that it would seek changes to a draft of the deal which had been agreed after months of negotiations with Washington.
The current draft is understood to allow Iraq to try American troops for serious crimes committed while off-duty and off base, something Iraqi officials have described as a major concession from Washington.
Washington has also agreed to withdraw its combat forces from Iraqi towns and cities by June 2009 with a complete pullout in 2011, eight years after the invasion that forced Saddam Hussein, the former president, from power.
The protest came as bombings in Baghdad killed an Iraqi army brigadier general and another soldier.
Police and hospital officials said a bomb attached to a car exploded near Andalus Square in the centre of the capital, killing the general and wounding his guard and a civilian bystander. The soldier died when a roadside bomb hit his patrol.