The journalist threw two shoes at Mr Bush as he shook hands with Iraqs prime minister, Nouri al-Maliki, during a press conference in Baghdad.
The man, who was sitting in the third row jumped up and shouted: It is the farewell kiss, you dog, and threw his shoes one after the other towards the president.
Mr Bush ducked the first one, while the second narrowly missed him.
Shoes soles are considered the ultimate insult in Arab culture.
The two leaders signed a security accord which calls for American troops to pull out of Iraq by the end of 2011.
President Bush had earlier described the war he started nearly six years ago as hard but essential for the security of Americans, Iraqis and for world peace.
Mr Bush visited Baghdad just 37 days before he hands over to President-Elect Barack Obama, who has pledged to end the war and was partly elected because of his opposition to it.
Speaking after two hours of meetings with Iraqi leaders, Mr Bush defended the conflict, saying: "The work hasn't been easy, but it has been necessary for American security, Iraqi hope and world peace."
He added: "I'm just so grateful I had the chance to come back to Iraq before my presidency ends." He then went on to stage a rally with US troops.
Hittttt!!!! lmao...wa him duck fast ee...how d second one miss him..Me mad at d yute weh through d show missing twice...Him shoulda black him face up wit D show mek we laff see bush inna D place wit a black eye lmao