Somali lawmakers voted overwhelmingly to dismiss Aden during a meeting of the interim parliament in Baidoa.
Aden made attempts last year to reach a peace agreement between Somalia's transitional government and the country's Islamic movement, which at the time controlled the capital, Mogadishu.
Ethiopian troops entered Somalia last month to support the transitional government, driving Islamist fighters from Mogadishu and much of the rest of the country.
Since then, U.S. officials have been urging government leaders to reach out to Somalia's fractured groups in an effort to end 16-years of conflict.
U.S. Assistant Secretary of State for African Affairs, Jendayi Frazer, says the decision to dismiss the parliament speaker hurts efforts to reconcile Somalia's factions.
"The symbol of the president and the prime minister backing a move to push him out is counter to that spirit of reconciliation," he said. "So we are advising the government, as supporters of the government, to demonstrate something different."
Frazer made her remarks during a forum on Somalia at the Center for Strategic and International Studies in Washington.
Also in attendance was Idd Beddel Mohamed, a representative of the Somali government to the United Nations.
Mohamed defended the decision to remove the parliament's speaker.
"It is the prerogative of the Somali parliament to decide what is good for Somalia," she said. "The speaker of parliament has put a motion against the prime minister twice and he failed miserably. What goes around comes around. Now he lost the vote of confidence and I hope the international community will respect the decision."
Despite the vote in parliament, Frazer says the United States continues its strong support for the interim government, saying Somalia now has the best chance to regain stability since warlords overthrew a dictator in 1991.
Frazer says Somalis are tired of war and ready for peace.
"Most important is the path of peace, reconciliation and stability," she added. "To a great extent, this process will rely on the government's willingness to reach out and create an inclusive political process. This objective, frankly, remains our greatest challenge."
The U.S. has pledged $40 million for humanitarian assistance and redevelopment.
Part of that money will be used to fund an African stabilization force that Frazer says will hopefully begin to arrive in Somalia within the next few weeks.