Under the agreement, Mahamat Idriss Deby's Transitional Military Council and hundreds of opposition representatives will launch a national peace dialogue in the capital N'Djamena on August 20.
The dialogue aims to agree the schedule and rules for a presidential election that military ruler Idriss Deby has promised by October.
However, few of the groups who took part in the talks, or the diplomats who monitored the painstaking negotiations, expect an election this year.
But after five months of mediation efforts by Qatar, the main rebel Front for Change and Concord in Chad (FACT) announced hours before the ceremony at a Doha hotel that it would not sign the deal.
UN Secretary General Antonio Guterres and the African Union urged the junta and opposition to seize the latest opportunity to stabilise a country considered key to international efforts to stamp out Islamic extremists in the Sahel region.
Deby promised a national dialogue and elections within 18 months of him seizing power, but the mediation has been fraught with discord.
FACT and other opposition groups have demanded that he announce that he will not stand in the election. Deby has said this can only be negotiated in N'Djamena.
He has also said his transitional rule could be extended but faces pressure from the international community to keep the deadline.
In a video message to the ceremony, UN Secretary General Antonio Guterres called the signing "a key moment for the Chadian people" but said the national dialogue had to be "inclusive" to be successful.
African Union Commission chief Moussa Faki Mahamat said that both sides keeping their promises would be "crucial criteria" to build trust with the Chadian people.
Qatar's Foreign Minister Sheikh Mohammed bin Abdulrahman bin Jassim Al Thani said the accord aimed to establish "a peace to replace the trouble and strife that the country has known for many long years".
Forty-three of the 47 groups who remained at the end of the mediation signed the accord to start national talks in N'Djamena on August 20.
Mahamat Zene Cherif, the interim government's foreign minister, acknowledged that there had been "difficult talks" in Doha but said he believed there was now a chance for "sustainable peace" in the country of 16 million people.
Cherif said he was "a little bit shocked" that the FACT rebels had not signed the accord but insisted that all armed groups could take part in the dialogue.
Groups who signed the accord committed to a ceasefire while the government has guaranteed the security of all those who return from abroad to take part in the talks.
UN Secretary General Antonio Guterres and the African Union urged the junta and opposition to seize the latest opportunity to stabilise a country considered key to international efforts to stamp out Islamic extremists in the Sahel region.