The vote on Tuesday has given the deal a needed boost ahead of a signing ceremony later this month.
The agreement, to take effect on 15 August, calls for most Indonesian soldiers to withdraw from the province by mid-September. The rebels must give up their demand for independence in return for some form of political representation in Aceh.
Initially, some parliament members criticised the deal and said the Free Aceh Movement (GAM) would use the lull in fighting to build up its forces.
But on Tuesday, parliament leaders came out of a meeting with President Susilo Bambang Yudhoyono and said they would endorse the agreement.
"The [parliament] supports the government efforts to end the conflict in Aceh in a peaceful, comprehensive and honest way that is within the framework of the unitary state of Indonesia and in accordance with the constitution," said Agung Laksono, the parliament speaker.
"The peace deal will speed up the rehabilitation and reconstruction process of Aceh following the tsunami."
Government negotiators and representatives of the Free Aceh Movement agreed in Finland last month to end the war in the province that has left more than 15,000 dead.
"The peace deal will speed up the rehabilitation and reconstruction process of Aceh following the tsunami"
The two sides were urged to end the conflict, after the December tsunami killed more than 131,000 people and ravaged the province on the northern tip of Sumatra.
While the accord has been praised as the best opportunity for decades for peace in the province, analysts warn disagreements over its implementation in the field and hardliners on both sides may well scuttle it.
Aside from the political participation issue, the Helsinki agreement carries provisions for amnesty, disarming the GAM, withdrawing Indonesian troops and monitoring by officials and soldiers from the European Union and Southeast Asia.
"On amnesty and political parties, that would depend on the existing regulations. Based on the agreement, there is still time in the next one to one-and-a-half years to discuss that," Laksono said.
The Swedish Rescue Services Agency said on Monday that it will dispatch an eight-member team to Aceh.
The Swedish team will provide logistical support for observers due from the European Union to monitor a peace accord between Indonesia and the separatist rebels from the GAM.
The EU and the Association of Southeast Asian Nations (Asean) were due to send 200 observers to monitor the treaty.
The tsunami left 170,000 people
dead or missing in Indonesia
The Swedish government has allocated 40 million kronor ($5.2 million) for the Swedish mission aimed at organising offices, transport, telecommunications and internet facilities for the observers.
The rescue agency said the Swedish team would likely leave on Wednesday for Indonesia.