A government military commander said later that Ras Kamboni was taken after a two-day campaign using ground forces and air support.
Mohammed Adow, Al Jazeera's correspondent in Somalia, said: "Taking over Ras Kamboni denies Islamist fighters a base from which to launch their guerrilla attacks.
"It leaves them sandwiched between the US forces patrolling the coast and Kenyan forces stationed at the border."
Yusuf's entry into Mogadishu marked a remarkable turnaround in the Somali capital that the Islamic courts ruled for six months until the end of December.
"The president has arrived. He is now in Villa Somalia," Abdirahman Dinari, the government spokesman, said.
The bullet-scarred Villa Somalia compound is the former palace of Mohamed Siad Barre, whose overthrow in 1991 as Somalia's last national president triggered more than 15 years of anarchy.
The UN-recognised transitional authorities had been unable to install itself in Mogadishu first because of local commanders in the government who opposed giving up their turf, and later because of the Islamic courts.
Adow said: "There are many government soldiers on the streets [of Mogadishu], but underneath it looks as though no one is in charge."
The Ethiopians have said they want to pull out of Somalia in a matter of weeks, while an African peacekeeping force is being assembled to fill the anticipated vacuum in security, which the Somali transitional government admits it cannot handle on its own.
In Addis Ababa, the Peace and Security Council of the African Union (AU) agreed to increase the number of troops to be deployed to Somalia from a proposed 8,000-strong deployment.
An official said on Monday the AU would meet again to decide on how many.
"The security council underlined the need for an urgent deployment of peace support mission to Somalia," Said Djinnit, the AU's peace and security commissioner, said.
Djinnit said: "The council also stressed the need for an all-inclusive political process as called for in [the Somalia] charter."
He said the meeting had called on other countries to fund the peace mission.
Abdikarim Farah, Somalia's ambassador to the AU, said the deployment of peacekeepers would require $150m for the first six months.
The US said on Friday that it was contributing $16m and the European Union has said it would also contribute.
Louis Michel, the EU aid commissioner, said in Brussels: "But first of all we want to know which kind, which troops, how many people, which mandate, and so on."