The Ulster Volunteer Force (UVF) and Red Hand Commando (RHC) said all arms and explosives were totally and irreversibly beyond use.
The Ulster Defence Association (UDA) also disclosed it had started to decommission its own haul of guns.
The organisations killed almost 1,000 people, mainly Catholics, during 30 years of violence.
The UDA said: “The dark days are now behind us and it is time to move on. There is no place for guns and violence in the new society we are building. It is time to work for a better future.”
The UVF said the process began last autumn, but was suspended after dissident republicans killed two soldiers and a policeman in Antrim and Craigavon, Co Armagh, in March.
It continued: “Assurances were sought from the Government and from the Irish Government that those responsible, in whatever jurisdiction, would be vigorously pursued and the failures of 1969 (when the conflict began) would not be revisited upon our community.
“Only when forthright assurances were given and it became clear that they would be honoured did our process resume.”
The group’s campaign of violence stretches back to the mid-1960s after the 50th anniversary of the 1916 Irish Rising and against calls for full civil rights for Catholics in Northern Ireland.
Dawn Purvis, leader of the UVF-aligned Progressive Unionist Party (PUP), said: “This is a truly momentous day in the history of progressive loyalism. The decommissioning of all weapons by the UVF and RHC shows that peaceful, stable, inclusive democracy is the way forward.”
While the Democratic Unionist Party (DUP) had met with loyalist groups, she made an apparent sideswipe at reports the party played a key role in delivering decommissioning.
“For those involved, decommissioning was a process, carefully managed and brought to fruition, not an event, and contrary to some reports, not delivered as a result of two meetings in the space of nine months,” said the PUP Assembly member.
Former UVF prisoner Billy Hutchinson helped negotiate with the Independent International Commission on Decommissioning (IICD) led by General John de Chastelain who four years ago witnessed destruction of the IRA’s arsenal of guns, ammunition and explosives.
“The war is over, the weapons have been put beyond use and we move on and I think that it’s quite clear,” Mr Hutchinson said.
“The Government and the Dublin government and the Executive (in Northern Ireland) have no excuses, loyalist weapons have been put beyond use.”