Sattah al-Batat, who led Friday's prayers, told worshippers the agreement "would give full authority to the Americans as well as the right to do whatever they want".
"As long as Moqtada Sadr rejects the agreement, it will not be signed" by the government, Batat told worshippers.
Bush and Nuri al-Maliki, the Iraqi prime minister, have agreed in principle in November to sign the Status of Forces Agreement by the end of July.
But negotiations appeared to have stalled earlier in the week as Iraq has a "different vision" from the US over the plan, according to Ali al-Dabbagh, an Iraqi government spokesman.
Al-Sadr has vowed to keep up a campaign of protest to pressure the government to relinquish the agreement.
Also on Friday, two leaders of "special groups" - a term used by the US military to describe Shia fighters who have defied al-Sadr's ceasefire - surrendered to US forces, according to a US military statement.
The surrenders took place when US forces raided their homes, south of Baghdad.
One of the men is alleged to have ordered attacks on US troops, directed the kidnapping of Iraqis and helped smuggle Iranian weapons into Iraq, the US military statement said.
The arrests and the Sadr City demonstrations came on the eve of al-Maliki's trip to Iran, the prime minister's second such visit in a year.