Ivory Coast has recently accused Gbagbo loyalists based in neighbouring Ghana of carrying out cross-border raids to destabilise the government of President Alassane Ouattara.
The courtroom in the buildings of the Court of Appeal was packed for the start of Gen Ble's trial. Gen Ble, who is from the same ethnic group as Mr Gbagbo, became the dominant military commander during the 2011 battle for control of Abidjan, operating from a well-fortified base at the presidential palace in the centre of the city.
He was one of the few generals not to switch allegiance to President Ouattara as the fighting came to a close.
Human rights activists have welcomed his trial but warn that it must appear to be fair otherwise it could further heighten political tensions in Ivory Coast.
Gen Ble has not yet entered a plea.
Colonel-Major Adama Dosso disappeared on 12 March 2011, at the height of the post-election crisis.
Prosecutors say he was kidnapped and then taken to the Republican Guard base, where he was allegedly interrogated by Gen Ble.
Col Dosso's body was later found, riddled with bullets, in a grave near the country's main highway.
There had been speculation that Col Dosso was about to pledge allegiance to Mr Ouattara.
On Monday, Mr Gbagbo's former spokesman Justin Kone Katinan was charged with murder linked to the post-election violence by the Ghanaian authorities, paving the way for his extradition.
Gen Ble was also charged in a separate case on Monday by a military court - over the 2002 killing of former coup leader Gen Robert Guei, a bitter rival of Mr Gbagbo.
Mr Gbagbo was arrested in April 2011 by pro-Ouattara forces backed up by UN and French troops.