Mr Deby's government blames Sudan for inspiring the uprising - an accusation Sudan denies.
Deby did not rule out the possibility of his country's troops returning under a U.N. mandate.
The standoff ended in 1990, when Mr Habre was toppled by the Libyan-backed Idriss Deby.
Sudan accuses Mr Deby of supporting the Sudanese rebels in Darfur who belong to his ethnic group.
Up until last year, Chad's President Idriss Deby provided Mr Bozize with his personal guards, she said.
Mr. Deby Itno, Chad's president, has exhorted Malian troops to join the battle for their country's sovereignty.
By the mid-1990s the situation had stabilised and in 1996 Mr Deby was confirmed president in Chad's first election.
Mr Deby has survived two attacks on the capital - in 2006 and 2008 - from rebels in eastern Chad.
Chadian President Idriss Deby announced his forces would not be sticking around for a protracted guerrilla war with the radical Islamic insurgents.
Mr. BUCHBINDER: France has backed the Deby administration militarily in the past.
"Mr Djotodia will not be called president of the republic, but head of state of the transition, " it quotes President Deby as saying.
BBC: Central African Republic neighbours to send 2,000 troops
On Monday, the Security Council did pass a resolution condemning the rebel advance and calling for governments to extend support to President Idriss Deby.
Chad President Idriss Deby, who attended the signing ceremony, said the deal would allow Mr Bozize to complete his mandate, which expires in 2016.
The announcement follows Friday's declaration by Chadian President Idriss Deby that his troops had also killed Abdelhamid Abou Zeid, another top rebel leader in Mali.
Chad, which has been ruled by Idriss Deby since 1990, has been ranked by Transparency International as one of the most corrupt countries in the world.
"It seems impossible to us to recognise a man who has appointed himself, " said Chadian President Idriss Deby following the emergency summit hosted in Chad's capital, N'Djamena.
But Chad will be important to France, and Chad will be a partner to France, whoever is running the government, be it Deby or one of these rebels.
The Sudanese government actually sponsored President Deby in his insurgency.
At home, President Deby Itno faces political pressure to justify an intervention half a continent away, criticism that some analysts suspect has goaded the government into exaggerating it's kills.
But I think the key thing, though, is that Chad has a closed political system and it has had a closed political system since long before Deby came to power.
Confusion continues to surround the fate of both Abou Zeid and Mokhtar Belmokhtar, but Chad's President Idriss Deby appeared on television on Monday evening to insist that both men were dead.
BBC: Islamist commander Abou Zeid's death in Mali 'probable'
Ms. WOODS: Well, Michel, let's remember, this all started back in 2005 when the Deby government essentially decided to change the Constitution so that he could run for a third term.
They have played a critical role, both in putting Deby into power in the 1990, and now seem to be ready to play a role in keeping him in power even today.
"Another thing was probably that President Bozize was starting to pursue alliances with other countries, notably South Africa - and that this was seen a compromising somewhat his relationship with Deby, " she said.
"One of the things that really frustrated President Deby was the presence of a Chadian rebel group on Central African territory and Deby's sense that Bozize didn't do enough to deal with this group, " Ms Lombard told the BBC's Newsday programme.
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