"This is the first time that such a declaration of cessation of hostilities is signed," Pasteur Habimana, a spokesman for the FNL, said.
"For Palipehutu-FNL [the rebel movement's political branch], this means the war stops forever," he said.
General Evariste Ndayshimiye, chief government negotiator and top military aide to President Pierre Nkurunziza, signed the agreement for the government side.
FNL leaders have returned to Bujumbura from exile to resume talks.
A ceasefire agreement was reached between the two sides in 2006 but it was never implemented.