Jawad al-Bulani, a Shia, was chosen to lead the interior ministry.
In order to satisfy several leaders within his coalition, al-Maliki had put forward two candidates for the interior ministry post.
Al-Bulani is a former air force engineer and told parliament that he left the armed forces in 1999. In 2004, he was a deputy member of Iraq's interim governing council set up after the US-led invasion. He was also a member of parliament in 2005.
The interior ministry was heavily criticised under the previous minister, whom Sunni leaders accused of sanctioning death squads, a charge he denied.
General Abd al-Qadir Jasim al-Ubaidi, a Sunni, was approved as defence minister. He served in the army under Saddam Hussein but was demoted when he opposed the invasion of Kuwait in 1990.
Al-Ubaidi told parliament he retired from the army in 1992 and two years later was arrested and put before a military court.
When Saddam was toppled in 2003, he joined the new Iraqi army and became commander of its ground forces.
"I never belonged to any of the present political groups," al-Ubaidi told the assembly. "I do not carry any sectarian title. I'm here for all Iraqis, not for one sect."
The two main security jobs were left temporarily vacant when al-Maliki's government of national unity took office on May 20 because his coalition partners were unable to agree on candidates.
Agreement has also been reached for Shirwan al-Waili to become the new minister for national security.
Al-Maliki has said he wanted to choose non-sectarian ministers to run his national unity government.