After the fall of Saddam Hussein's regime in April 2003, Jaafari returned to Baghdad and actively participated in the political reconstruction of Iraq. In July of the same year, the Iraqi Governing Council was established, and Jaafari became one of the nine members of the Presidium of the Governing Council. In August 2003, Jaafari served as the first chairman of the Interim Management Committee.
In the early days of the establishment of the Governing Council, Arab countries were once cautious about the Governing Council and repeatedly refused to recognize the Iraqi Governing Council. In order to gain the support of Arab countries, Jaafari led a delegation of the Management Committee to visit the United Arab Emirates, Bahrain, Kuwait, Oman, Saudi Arabia and Egypt, and received a positive response.
Jaafari's political views have always been moderate and pragmatic. After the war, bloody conflicts continued in Iraq, and the interests of various factions were seriously entangled. However, he has always insisted that the use of force to solve Iraq's domestic problems is not the best way, and the possibility of peaceful settlement should be considered. He also opposed malicious revenge between races. These moderate ideas won him a deep public opinion base and inner-party support. At the beginning of June 2004, the Iraqi interim government was established, and Jaafari became the vice president of the Iraqi interim government.
In the Iraqi general election held on June 30, 2005, Dawa Party, with Jaafari as the general secretary, as one of the main political parties of the Shiite "Iraqi United Alliance", participated in the competition for seats in the transitional parliament. The "Iraqi United Alliance" won 140 seats in the 275 seats in the parliament. On February 22nd, "Iraqi United Alliance" formally nominated Jaafari as the prime minister candidate of the Coalition's transitional government. On April 7, Jaafari was nominated by the Iraqi Presidential Committee as the Prime Minister of the Transitional Government and was responsible for forming a cabinet. The Transitional National Assembly of Iraq adopted the list of members of the transitional government he submitted on the 28th. On May 3, the Iraqi transitional government led by Jaafari was sworn in in Baghdad.