The region's human rights ombudsman, Gigham Stepanyan, said there were "at least 200 dead and more than 400 wounded" in the operation, which began on Tuesday and ended on Wednesday with a ceasefire deal after the separatists surrendered.
According to media reports, Armenians in the Nagorny Karabakh region agreed to Azerbaijan's conditions for their disarmament to stop the military operation.
Russia's Interfax news agency reported that Armenian separatists in Nagorno-Karabakh had agreed to the terms of a ceasefire proposed by Russian peacekeepers after suffering a series of battlefield setbacks at the hands of Azerbaijan's army.
The ceasefire took effect at 9 a.m. on Wednesday, with talks scheduled for Thursday on reintegration with Azerbaijan.
Later, the Azerbaijani presidency confirmed negotiations on Thursday on the reintegration of Nagorny Karabakh with Azerbaijan.
Azerbaijan's Defense Ministry also confirmed on Wednesday that it had reached a ceasefire agreement with ethnic Armenian forces in the Nagorno-Karabakh region.
The ministry said Armenian forces in the mountainous region had agreed to "lay down their arms, abandon combat and military positions and completely disarm" and that all weapons and heavy equipment were being handed over to the Azerbaijani army.