The visit came as a wave of explosions hit the northern city of Kirkuk, killing at least 16 people.
President Bush met with al-Maliki and other officials in the heavily fortified green zone at a palace once used by Saddam Hussein and now serving as the U.S. Embassy.
The leaders had gathered there in expectation of a video conference with the president and other U.S. officials, supposedly at Camp David in Maryland. The video conference will proceed but with the president at al-Maliki’s side, reported the Associated Press.
President Bush also was expected to meet with Iraqi President Jalal Talibani, the speaker of parliament and U.S. troops.
“Good to see you,” said al-Maliki, who was unaware of President Bush’s visit until five minutes before his arrival.
“Thanks for having me,” the president replied as the two shook hands.
The visit came six days after the death of al-Qaida in Iraq leader Abu Musab al-Zarqawi, who was killed in a U.S. air strike.
U.S. officials called the death a significant step in the war on terror but said they expected violence in Iraq to continue.
President Bush is under pressure to start reducing the 132,000 American forces in Iraq, but he has said troop withdrawals are dependent on Iraq’s ability to provide its own security.
Al-Maliki has pledged to crack down on militias and sectarian violence, promote national reconciliation, boost reconstruction efforts and restore essential services such as electricity, according to the AP.
Accompanying President Bush on his trip were national security adviser Stephen Hadley, chief of staff Joshua Bolton, deputy chief of staff Joe Hagin, press secretary Tony Snow, White House counselor Dan Bartlett and several others.