Sign of contempt
In Iraqi culture, throwing shoes at someone is a sign of contempt.
The incident will serve as a vivid reminder of the widespread opposition to the US-led invasion of, and subsequent war in, Iraq - the conflict which has come to define Bush's presidency.
Bush shrugged off the incident and quipped: "All I can report is that it's a size 10."
Adil Shamoo, an Iraqi analyst at the Institute for Policy Studies in Washington DC, told Al Jazeera: "I think we should go beyond the shoe and think about the fact that the US should respect Iraq's sovereignty in order to regain respect of the Iraqi people and the Arab world.
"I think Bush has increased terrorism against the United States and instablity in the Middle East because of his policies."
The US president was in Baghad for unannounced talks on the pact between Iraq and Washington that will see American troops leave Iraq by 2011.
Al-Maliki applauded security gains in Iraq and said that two years ago "such an agreement seemed impossible".
Bush's visit to the Iraqi capital came just 37 days before he hands the presidency over to Barak Obama, who has vowed to withdraw troops from Iraq.