Adebolajo, 28, from Romford, and Adebowale, 22, from Greenwich, have both been accused of killing Fusilier Rigby, in Artillery Place, as he returned to Woolwich Barracks, where he was stationed.
Rigby died on 22 May this year, following an attack that left him with multiple cut and stab wounds.
The hearing, which took 45 minutes, was attended by members of Rigby's family.
As reported by the Independent, the two accused, however, were not in court, but took part in the hearing via separate video-links from HMP Belmarsh, the high-security jail where they are being held.
According to the London Evening Standard, Adebolajo and Adebowale also pleaded "not guilty to conspiring together to murder a police officer." The
paper also reports that the two men "denied separate charges of attempting to murder a police officer on the same day."
Adebolajo asked to be known by the name Mujahid Abu Hamza while Adebowale asked to be known by the name Ismail Ibn Abdullah.
The pair will remain in custody until their trial, which,
according to the Guardian, has been scheduled by the judge, Mr Justice Sweeney, to begin at the Old Bailey on 18 November 2013.