"We believe that this new arrangement - and our allies as well, because they have agreed to it - will provide greater predictability, continuity, stability in this volatile important region of Afghanistan," Morrell said.
The commitment falls short of a proposal favoured by General Dan McNeill, the commander of the Nato-led force in Afghanistan, that a single country be put in charge of military operations in the south.
McNeill and others have said that a lack of continuity has limited the effectiveness of the Nato-led International Security Assistance Force (Isaf) in the south.
Not only do the commands currently change hands every nine months, but European troops that serve in the south rotate every three to six months.
"It is sometimes a little difficult for [Afghan forces] to change from one culture to the next," McNeill said on Wednesday.
Another unresolved issue is whether to continue having two US four-star generals responsible for the 33,000 US troops serving in Afghanistan.
General John Bantz Craddock, Nato's supreme commander, is responsible for the 50,000-strong Isaf, which includes 15,000 US troops.
General David Petraeus, who has been tapped to be the next head of the US Central Command, will be responsible for another 18,000 US troops conducting counter-terrorism and training missions in Afghanistan.
"That is probably the last large remaining issue to be dealt with, whether it makes sense to ... dual-hat a commander down there or keep the command divided," Morrell said.