People across the UK were invited to mark the occasion at their homes, on their streets and with community events from 8pm.
Throughout Sunday, hundreds of people flocked to the village of Hillsborough to lay flowers at the gate of the castle, the royal residence in Northern Ireland.
Thousands are believed to have visited the front gates of Hillsborough Castle ahead of the moment of reflection on the life and legacy of the late monarch.
A gong was sounded as the minute’s silence began, prompting the crowd to bow their heads as they stood in front of floral tributes left at the gates of the castle.
Fiona and Peter Moore, from Ballygowan, told the PA news agency they went to Hillsborough to pay their respects.
“Just over the years, she’s just always been a very solid figure, always there, and it’s just a bit of a shock, really, at the end when eventually it’s come to her passing on. We’re very sad to see that,” Mr Moore said.
Marky Pritchard, originally from Lurgan but who now lives in Royal Hillsborough, said he and his family are flying to London on Monday morning to attend the funeral.
She's the commander in chief, commander in chief then, and the commander in chief of my heart now, and always will be
“She meant everything,” he said.
“When I was 16 years of age I swore an oath to the lady and I meant every word of it,” Mr Pritchard said, who serves with The 1st Battalion of the Royal Irish Regiment.
“So it’s quite emotional. She’s the commander in chief, commander in chief then, and the commander in chief of my heart now, and always will be.”
Robin Campbell, from Hillsborough, said he came out on Sunday night “to join with the rest of the nation for the minute’s silence for the Queen, to remember her”.
“It’s such an historic event, sad but also celebratory in that she’s also left a great legacy for us all to follow,” he said.
In Belfast, people gathered at the mural of the Queen on the Shankill Road and West Belfast Orange Hall’s memorial garden ahead of the minute’s silence.
William Humphrey, chairman of the West Belfast Orange Hall Committee and a former member of the Northern Ireland Assembly, told those gathered at the Orange Hall that the Queen was respected “not just as our monarch, but as an international stateswoman”.
“We will never see the like of her again. Tonight we are gathered here to join with the rest of the nation in that one-minute silence.
“We have lost someone who, for many of us, started off as the daughter of this nation, became the mother of our nation, the grandmother of our nation, and the great-grandmother of our nation.
“I think it’s fair to say that for all of us, and that’s right across the country, the Queen’s passing was like someone in our own family passing, and I think that pays tribute to how she was loved across every household in the kingdom.”
Members dressed in their orange collarettes then bowed their heads during the minute’s silence.
Afterwards, a flautist played Abide With Me for those gathered in front of the illuminated building and a short service was held.
The silence was also observed in other venues across Northern Ireland, including at Belfast International Airport and the landmark tourist attraction Titanic Belfast.
A cross-community service of prayer and reflection was held from 6pm at St Macartin’s Church of Ireland Cathedral and at St Michael’s Catholic Church in Enniskillen, Co Fermanagh, where the congregation retraced the path the Queen took from one church to the other during her 2012 visit.
Hundreds of foreign dignitaries and charity representatives will be among those who will join the royal family at the Queen’s funeral at Westminster Abbey on Monday.
They will be bussed to the venue from early morning, with the service expected to begin at around 11am.
Events are being held across Northern Ireland where people can watch the state funeral, including at Coleraine Town Hall and Belfast City Hall.
Large screens will also broadcast the funeral live in the People’s Park in Ballymena and Shaftesbury Park in Carrickfergus.
The funeral comes almost a week after the King made his first visit to Northern Ireland as the UK’s new head of state.
Charles met politicians at Hillsborough Castle before he and the Queen Consort attended a memorial service in the Queen’s honour at St Anne’s Cathedral in Belfast.
Charles and Camilla also greeted some members of the public who had gathered to catch a glimpse of the new monarch.