The government and the Free Aceh Movement (Gam) signed the agreement on Monday after six months of talks.
Mr Yudhoyono also spoke of finding a solution to another ongoing separatist conflict, in the province of Papua.
He made the remarks in an annual speech to parliament, a day before Indonesia marks 60 years of independence.
Mr Yudhoyono told parliament on Tuesday that everything agreed in the Aceh peace deal would be implemented on the ground.
Representatives from both the government and Gam signed the official peace accord in Helsinki on Monday.
In a commentary article for the International Herald Tribune on Tuesday, Mr Yudhoyono described the peace agreement as "a victory for the Acehnese, who have suffered for so long."
"We now have a golden opportunity to change Aceh for good. We cannot afford to squander it, because a chance for permanent peace does not come often in history," he wrote.
During his speech, Mr Yudhoyono also spoke about Papua, formerly known as Irian Jaya, which has been a scene of secessionist violence since Dutch colonial rule formally ended in 1962.
Mr Yudhoyono ruled out independence for the area, but said a solution involving a form of special autonomy needed to be sought.
"The government wishes to solve the issue in Papua in a peaceful, just and dignified manner, by emphasising dialogue and a persuasive approach," Mr Yudhoyono said.
"The policy for the settlement of the issue in Papua is... special autonomy, as a just, comprehensive and dignified solution," he told parliament.
He emphasised that the situation would be solved without foreign interference.
He also rejected criticism that, by allowing international monitors to assess the progress of the Aceh peace deal, Indonesia was giving foreigners too big a role.
Taken from BBC News
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