Connolly was remanded in custody after being brought before the court and charged over the shooting of the notorious criminal near his home on Dublin’s northside.
Gangland ‘Godfather’ Kelly (65) was shot several times in broad daylight on Furry Park Road, Killester on Tuesday.
He was involved in serious crime spanning 40 years and had links to a number of major city criminals, including slain mob boss Eamon ‘the Don’ Dunne.
Connolly was last night charged with murdering Kelly, as well as possession of a Glock semi automatic pistol with intent to endanger life, and membership of an unlawful organisation – the IRA.
The accused, with an address at Bernard Curtis House, Bluebell, is charged with the offences at Furry Park Road on December 4.
He gave the thumbs up to supporters in the courtroom yesterday evening before being remanded in custody for two weeks.
Detective Sergeant Enda Mulryan told the court he arrested the accused at All Saints Drive, outside Raheny Garda Station under the Offences against the State Act.
Connolly was then brought to court and had "nothing to say" to each charge after caution. He was handed a copy of the charge sheets.
The court heard the DPP had directed that he be charged before the Special Criminal Court.
After Det Sgt Mulryan gave evidence, each charge was read out to the accused in court.
State Solicitor Michael O'Donovan applied for a remand in custody.
Connolly's barrister, Anne Marie Lawlor, consented to this and said she had "no difficulty with his attendance by way of video link".
The defendant was remanded in custody to appear in court again on December 20. Ms Lawlor said a legal aid application would be made.
Connolly, wearing a light grey Adidas tracksuit, did not speak during the brief hearing.
When proceedings were over, he raised a thumb in the direction of supporters in the public gallery.
After the hearing ended, Connolly was taken to Portlaoise Prison by gardai and members of the defence forces.
Kelly, a career criminal whose death was the 15th gun murder of the year, escaped a 2010 attempt on his life when his attacker's gun jammed.
Dubbed the Godfather, Kelly was jailed for 14 years in the 1990s for possession of a kilo (2.2lb) of cocaine and was sentenced for assaulting a Workers Party member in the late 1980s.
In recent years he had been portrayed as a close associate and confidant of ruthless gang leader and drugs boss Eamon 'The Don' Dunne, who was shot dead in a pub in Cabra, north Dublin, in 2010.
The father-of-nine was said to have cut his teeth as an armed robber working with the Official IRA in the 1980s, raising money for the paramilitary group.
Detectives are investigating a possible link to a bloody dispute with the Real IRA in north Dublin.
Their leader, Alan Ryan, was murdered in September in a daylight gun attack. He had been embroiled in extortion and racketeering and demanding money from drugs gangs.