In the national election of December 2005, the UIA once again won the majority of the votes, which according the new Iraqi constitution, gets to pick the Prime Minister. UIA members voted for the Prime Minister with only two main candidates. Al-Jaafari was one and the SCIRI member
Adel Abdul Mahdi, a secular economist. Jaafari won the vote only by one (64 - 63). His win was credited to the support of
Muqtada Al Sadr's members of UIA, who all voted for him.
Despite this win, however, he became increasingly associated with the failure to end the violence in Iraq and to improve services. Because of this, the Sunni, Kurdish and secular groups in the parliament refused to agree to him continuing as Prime Minister, leading to deadlock. His refusal to stand down began to alienate even those who had backed him up to that point, but it is believed that only when
Ayatollah Ali al-Sistani intervened that he finally stepped down. The US government had expressed dissatisfaction with him in two months earlier, with
George W. Bush stating that he "doesn't want, doesn't support, doesn't accept" his retention as Prime Minister.
He was succeeded by al-Maliki as Dawa Party secretary-general in May 2007.