Hundreds of people attending a special service at the Co Fermanagh town's War Memorial fell silent at 10.43am on Thursday.
It marked the anniversary of the moment a no-warning IRA bomb detonated, killing 11 people and injuring over 60 others on Remembrance Sunday, 8 November 1987.
A twelfth victim, Ronnie Hill, died in 2000.
Wreaths were laid at the cenotaph by relatives of those who lost their lives.
First Minister Peter Robinson and Secretary of State for Northern Ireland, Theresa Villiers, also laid wreaths in tribute.
Lord Maurice Morrow told those who had gathered: "They were not soldiers answering for battle. They were not armed. They were not at the Cenotaph to harm or do anyone harm.
"They were deemed however to be legitimate targets because they wanted to honour those of all faiths."
A Service of Community Remembrance and Reflection followed at St Macartin's Church of Ireland Cathedral.
As we mark the twenty-fifth anniversary of the bombing at Enniskillen, my thoughts are with the victims, the bereaved, and with all those who continue to bear the scars of this dreadful event.
In his address, Bishop of Clogher, The Rt Revd John McDowell, said: "For all of us on 8 November 1987, whether near or far from Enniskillen, we were aware that something almost indescribably depraved had happened.
"That people who had gathered for a simple and dignified act of remembrance, had now, through some perverted ingenuity, themselves suffered the same bloody devastation that had been visited on those who they had gathered to remember.
"Today is a day when we remember those who were themselves remembering when they were murdered, and we try to do so with the same simplicity, gratitude and dignity as they showed when they gathered that day at the War Memorial."
Following the service, families of the bereaved were brought into a private room where a message was read from the Queen.
"A quarter of a century ago, we were able to draw comfort and strength from the hope that out of the personal tragedies of Enniskillen might come eventual reconciliation between communities", she wrote in her message.
"Today, a quarter of a century later, we can all reflect on how far we have travelled along this road; and my recent visit to the people of Enniskillen gave me much reason to be optimistic about the future.
"My good wishes and prayers are with everyone who will be marking today's anniversary, and with all those who strive for peace in this country and throughout the world."
The Poppy Day atrocity provoked outrage around the world after innocent people were murdered while remembering the war dead.
The names of the victims - who were all Protestant and included three married couples and pensioners - have been added to the town's cenotaph.
No-one has ever been convicted over the attack, but now there is hope a fresh inquiry can be launched.
On Sunday, a statement from the PSNI said: "The Historical Enquiries Team has concluded its work on the deaths which were caused at the Enniskillen Cenotaph bombing in 1987.
"Staff have updated families on the HET work and will formally hand over to PSNI's Serious Crime Branch who will assess the potential for further work to be progressed."
Mr Robinson called for anyone with information on the attack to come forward with it and had a message for republicans.
"They are keen to have reconciliation in Northern Ireland, they want people to have the truth yet they remain silent about what happened on this occasion," he said.
"Let those who want to have the truth speak the truth. I would be very keen that there would be some justice given to the families after such a long period of suffering and torment."