Speaking to the Reuters news agency by phone from Eritrea, Aweys said: "We encourage the insurgents and the Somali people not to be tired of combating the enemy."
Earlier, the Somali leader, who holds no formal position in the opposition alliance, told Mogadishu-based Shabelle radio: "I do not believe that the outcome of this conference will have any impact on the resistance in Somalia.
"The aim of the meeting was to derail the holy war in the country."
The United Nations had announced the terms of the Somali peace deal late on Monday.
Ahmedou Ould-Abdallah, an aide to the UN envoy for Somalia, said: "We have a peace deal."
"They agreed on the termination of all acts of armed confrontation ... to come into force 30 days from the signing of the agreement for an initial period of 90 days, renewable."
Ould-Abdallah said the agreement also called for the UN to authorise deployment of an international stabilisation force.
Within 120 days, Ethiopian forces helping the government fight the Islamic Courts' Union remnant fighters would then leave, conditional on the deployment of sufficient UN troops, he said.
Ban Ki-moon, the UN secretary general, welcomed the agreement and voiced hope that other Somali groups and individuals "will soon adhere to this agreement".
Meanwhile, clashes between Muslim fighters and Somali-Ethiopian forces killed at least 28 people over the weekend in Mogadishu.
The fighters are waging a campaign, similar to those in Iraq and Afghanistan, of roadside bombings, ambushes and assassinations.
The violence has triggered a humanitarian crisis that aid workers say may be the worst in Africa, with at least a million people displaced.