In all, 12 people have been arrested, including Adebolajo and Adebowale, in connection with the killing.
The commission will be led by Lord Adebowale, chief executive of the social enterprise Turning Point.
Addressing Adebowale, Chief Magistrate Howard Riddle said that he could sit rather than stand because he was injured.
Adebowale is also charged with unlawful possession of a firearm, a Dutch revolver, the Metropolitan Police said Wednesday.
Adebolajo and Adebowale, who officials familiar with the matter say were previously known to the country's security services.
Michael Adebolajo, 28 and Michael Adebowale, 22 are under guard in hospital after being arrested over Drummer Rigby's murder.
Adebowale appeared to walk uncomfortably and his right hand was wrapped in what could have been a medical dressing.
Adebowale was charged with murder after he was released from the hospital Tuesday.
CNN: Second suspect charged with murder in UK soldier's slaying
Adebowale's case has also been referred to the Old Bailey in London.
Another of the murder suspects, Michael Adebowale, 22, has been discharged from hospital and moved into custody in a south London police station.
Flanked by two police officers, Michael Adebowale spoke to confirm his name, his address and that he was aware of the charges against him.
Crossbencher Lord Adebowale said young adults were "significantly over-represented" in the prison population, with "very high" reoffending rates following often short periods in custody.
Lord Adebowale told the chamber that the vast majority of this category of offenders were men, and disproportionately from black or ethnic minority communities.
Both Mr Adebolajo and Mr Adebowale, Britons of Nigerian descent, are understood to be converts to Islam, with Mr Adebolajo originally coming from a Christian family.
Adebolajo and Michael Adebowale, 22, were hospitalized after the attack.
CNN: Second suspect charged with murder in UK soldier's slaying
Two men now identified by people familiar with the matter as 28-year-old Mr. Adebolajo and 22-year-old Michael Adebowale were shot and arrested by police that day and remain hospitalized and in custody.
"There is sufficient evidence to prosecute Michael Adebowale and it is in the public interest to do so, " said Sue Hemming, head of the Crown Prosecution Service's Special Crime and Counter-Terrorism Division.
Lord Adebowale told her the issue was unlikely to go away and said he would like the opportunity to discuss the matter further with the minister, before agreeimg to withdraw the amendment.
Mr Adebolajo, 28, originally from Romford, east London, and fellow suspect Michael Adebowale, 22, of Greenwich, south-east London, had been known to MI5 for eight years, Whitehall sources told the BBC on Thursday.
The magistrate referred Adebowale's case to a higher court -- the Old Bailey in London, also known as the Central Criminal Court -- where he will have a bail hearing June 3 and a further preliminary hearing June 28.
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