Previously a close ally of Laurent Gbagbo, Gen Phillippe Mangou fled his post with his wife and five children and sought refuge at South Africa's embassy.
Mr Gbagbo has refused to concede the presidency since losing November's elections. The move will damage Mr Gbagbo's chances of clinging to power following the disputed poll, as the Army is one of the key levers of power which had remained loyal to him and supported him in his bid to retain the presidency.
Gen Mangou's desertion came as Alassane Ouattara's Republican Forces took the key seaport of San Pedro on Thursday, and extended their zone of control to within close range of the commercial capital after a week of military advances from their northern strongholds.
Mr Ouattara called for all remaining pro-Gbagbo troops to lay down their weapons or join his side as Abidjan braced for battle.
Gunfire and heavy artillery was reported close to one of the city's main military barracks, and in the area where the Presidential Palace is located. It was unclear whether the clashes indicated that Republican Forces had entered the city. (read more)