Counsel Michael Karnavas said Blagojevic had not been involved in the crime, and that the prosecution had not produced evidence proving that Blagojevic had sent someone to commit the murder.
Karnavas said Blagojevic had not taken part in meetings at which General Ratko Mladic and other top military officials were deciding about the fate of the captured Muslims, but had been running from Mladic the whole time.
The counsel also argued the credibility of the testimony of repentant witness Momir Nikolic, who admitted to the crime in 2003, when he was sentenced to 27 years in jail.
Blagojevic, who does not recognise Karnavas as his counsel since the Hague tribunal banned him from changing counsel, distanced himself from the defence's closing arguments, saying he had not taken part in preparing them.
The prosecution asked for a 32-year prison sentence for Blagojevic.
Jokic's counsel Miodrag Stojanovic said he had not taken part in agreements to kill the Muslim captives and had no idea about it.
Jokic is charged with aiding and abetting in the shooting and burying of the Muslim victims.
Stojanovic refuted the testimony of repentant witness Dragan Obrenovic, who admitted guilt for the Srebrenica crime and was sentenced to 17 years' imprisonment.
For Jokic, the prosecution asked a 15-20 years jail term.
The Blagojevic-Jokic trial began on 14 May 2003. The main hearing ended in mid-July 2004. Blagojevic was arrested by the NATO-led Stabilisation Force in Bosnia-Herzegovina in August 2001, while Jokic turned himself in shortly thereafter.