The green zone, which houses Iraqi government buildings, and several major embassies in addition to US interests, is the target of frequent rocket and mortar attacks.
US officials declined to say exactly where the rocket landed, but an Iraqi police source said it struck near the sprawling US embassy complex.
US forces handed full responsibility for "entry control points" that regulate movement into and out of the area to Iraqi authorities on June 1, 2010.
Ceding control over entry points is part of the US draw-down, which will see troop numbers in Iraq cut from about 70,000 today to 50,000 by the end of August, ahead of a full withdrawal planned for 2012.
As part of the draw-down, US forces gave Iraqis control over the prison formerly known as Camp Cropper last week.
Four "terrorist" detainees with alleged links to al-Qaeda have since escaped from the prison on the outskirts of Baghdad, Dara Nurredin Dara, Iraq's justice minister, said on Thursday.
"They escaped two days ago," Dara said, adding that the prison's warden has also gone missing. He declined to say whether the warden was involved with the escape.
"An investigation is being carried out in order to find out what mistakes were made and who helped them," Dara said.
The disappearance of men "accused under anti-terrorism laws" is seen as a major embarrassment for the Iraqi government.
The US has refused to comment on the escape.