Hussein, who became Somalia’s prime minister in November 2007, has in the last few months been in dispute with Yusuf over efforts towards a peace deal with the Alliance for the Re-liberation of Somalia (ARS), the country’s main opposition group.
Yusuf said on Sunday that his move to sack Hussein and the entire cabinet was because the country was mired in instability.
The president needs parliament's approval to sack the prime minister, the Somali transitional government's federal charter says.
"It was difficult to work with the president, who disapproved of the peace process," Hussein said before the vote.
"The president was interfering with the activities of the prime minister and parliament.
"It is up to parliament to make a decision in order to save the transitional federal institutions and the rule of law."
Yusuf said on Monday that he would not try to undermine the parliament's decision.
'Peace effort threatened'
Hussein on Sunday said that the Yusuf had tried to destroy a UN-sponsored reconciliation process between the transitional federal government (TFG) and the ARS.
"The president abused the power of his office and undermined the legitimacy of parliament ... The president was attempting to sabotage peace efforts between TFG and the ARS," Hussein said.
Jean Ping, the African Union Commission chairman, said that disputes within the transitional federal government could derail peace efforts.
Yusuf's move to sack Hussein "has the potential of undermining the sustained efforts being made by the AU, IGAD and the larger international community, including the United Nations, to further reconciliation, peace, and stability in Somalia", the AU said in a statement.
IGAD is the Inter-Government Authority on Development, an organisation which has been involved in peace negotiations in Somalia and in the setting up of the country’s transitional institutions.
The latest parliamentary vote in favour of Hussein comes three months after he survived a vote of no-confidence in the wake of accusation that he had embezzled state funds.
The transitional government, which is based in Baidoa, has struggled to exert its influence across the rest of the country since it was established in 2004.
Somalia has been without an effective government since the overthrow of president Mohamed Siad Barre in January 1991 by rebel forces.