The agreement, reached on Tuesday after 10 days of tense negotiations, will enable Malian troops to enter the Tuareg-held city of Kidal in the north-east to secure polls scheduled to take place on July 28.
Malians have welcomed the truce but there are fears the deal will be difficult to implement and could unravel after the vote.
Malian military sources said the accord envisages the army entering the regional capital "without delay", accompanied by French soldiers and troops from the African-led International Support Mission to Mali.
France's President Francois Hollande told a meeting of his Cabinet that the agreement was "a major breakthrough", his spokesperson said.
The US also welcomed the deal.
"The agreement clears the way for the return of Malian administrative and security authorities to Kidal to permit the holding of presidential elections there on July 28," state department spokesperson Jen Psaki said.
And the UN Security Council urged other armed groups who had cut ties with "terrorist organisations" in Mali to join the ceasefire.
But analysts raised a number of problems with securing a long-term ceasefire, such as difficulties monitoring any disarmament; and differentiating Tuareg militants from the diverse range of insurgents infesting Mali's north.
Peace talks after the election
"Ultimately, this is an interim agreement to allow the organisation of the presidential elections in Kidal, " Malian analyst Mamadou Samake told Agence France-Presse.
"It has not solved all the problems, it just put off some of the problems."
The Malian government signed the accord with the National Movement for the Liberation of Azawad (MNLA) and a smaller Tuareg group in Ouagadougou, capital of neighbouring Burkina Faso.
The two sides agreed to halt hostilities and organise peace talks after the election, but the Tuaregs were not pressed to lay down their weapons.
"It was that or nothing, but we were heading for disaster if we hadn't been able to get an agreement on presidential elections in the Kidal region," said an aide to President Dioncounda Traore.
The Tuareg occupation of Kidal has been a major obstacle to holding the election, seen as crucial to Mali's recovery from the conflict of the past 15 months.
Malian officers staged a coup in March 2012 but the weak army was overpowered by the MNLA, which seized key northern cities before being sidelined by its al-Qaeda-linked allies.
The MNLA sided with a French-led military intervention, which reclaimed most of the lost territory from the rebels. But they have been reluctant to allow government troops into their Kidal bastion for the vote.
For analyst Samake, settling the major issues relating to Mali's Tuareg separatist movement will have to wait.
'Elections loom on the horizon'
"After the presidential elections, the legislative elections loom on the horizon. Former Tuareg rebels will certainly want to stand," he said.
"But for now, they cannot because of an arrest warrant against them … That could create problems."
Those warrants will likely be dropped, but the accord does state that international investigators will look into crimes against humanity and war crimes committed during the conflict.
Confronted with these problems, an official from the ministry of territorial administration would only say: "Let's take each day as it comes."
The logistics of the disarmament is another obstacle to be cleared for all parties working for lasting peace in the Kidal region.
But the larger problem, said military sources, is that Islamist insurgents continue to hide out in northern Mali. They could launch attacks which might be wrongly attributed to former Tuareg rebels.
"We are the military – we don't do politics," a battalion commander from a neighbouring country's army told AFP in the northern city of Gao.
"But just so there is no ambiguity, there will have to be some kind of mechanism in Kidal to prevent any infiltration of terrorists, otherwise it could complicate things." – AFP