George, 9, and Charlotte, 7, were seen walking into the church with Kate, while William joined the procession escorting the queen's coffin to the service.
The siblings then joined the procession at Westminster Abbey, walking in between William and Kate and their uncle and aunt, Prince Harry and Meghan, the Duchess of Sussex.
Following their great-grandmother's death, George is now second in line to the throne and Charlotte is third in line. Their father, William, is heir to the throne and their grandfather is now King Charles III.
George and Charlotte were the only great-grandchildren of the queen to attend the funeral.
"They’re viewing this through their eyes, little children’s eyes, but it’ll be a memory that stays with them forever, until it’s George’s time or it’s Charlotte’s time," said ABC News royal contributor Robert Jobson, adding of William and Kate's decision to allow their eldest children to take part, "I can see the wisdom in the decision because they’re going to remember this."
He continued, "They’re going to remember being a part of it. They’ve both seen it. They’ve witnessed it and have been part of it."
At the time of her death on Sept. 8, the 96-year-old queen was a grandmother of eight and great-grandmother of 12.
In addition to George and Charlotte, the queen was also great-grandmother to their younger brother, 4-year-old Prince Louis, and their cousins, Archie, 3, and Lilibet, 1, the children of Harry and Meghan.
The queen's other great-grandchildren include Savannah Phillips, 11, and Isla Phillips, 10, the daughters of Peter Phillips, the queen's eldest grandson and the son of Anne, the Princess Royal; the three children of Phillips' sister Zara Tindall, Mia, 8, Lena, 4, and Lucas, 1; the 1-year-old son of Princess Eugenie of York; and the 1-year-old daughter of Princess Beatrice of York.
The queen, who was known as "Granny" and "Gan Gan" by her grandchildren and great-grandchildren, was beloved by her family.
Five of her great-grandchildren were named for her -- William and Kate's daughter Charlotte, whose full name is Charlotte Elizabeth Diana; Lilibet "Lili" Diana Mountbatten-Windsor, the 1-year-old daughter of Harry and Meghan; Isla Phillips, whose middle name is Elizabeth; Lena Tindall, whose middle name is Elizabeth and Sienna Elizabeth Mapelli Mozzi, the 1-year-old daughter of Princess Beatrice and Eduardo Mapelli Mozzi.
In their remembrances of the queen, royal family members have spoken of the time she spent with them outside of the spotlight.
"Granny, while this final parting brings us great sadness, I am forever grateful for all of our first meetings—from my earliest childhood memories with you, to meeting you for the first time as my Commander-in-Chief, to the first moment you met my darling wife and hugged your beloved great-grandchildren," Harry said in a statement. "I cherish these times shared with you, and the many other special moments in between."
William said in a statement he was thankful his three children got to spend so much time with their great-grandmother.
"And while I will grieve her loss, I also feel incredibly grateful. I have had the benefit of The Queen's wisdom and reassurance into my fifth decade," William said. "My wife has had twenty years of her guidance and support. My three children have got to spend holidays with her and create memories that will last their whole lives."
The queen's youngest son, Prince Edward, recalled the joy of seeing the queen spend time with his children, James, Viscount Severn, 14, and Lady Louise Mountbatten-Windsor, 18, the queen's youngest grandchildren.
"Sophie and I have taken huge pleasure in seeing our James and Louise enjoying the places and activities that their grandparents loved so much," he said. "Given that my mama let us spend so much time with her, I think she also rather enjoyed watching those passions blossom. Those times together, those happy memories, have now become massively precious to each and every one of us."
The queen was known to have her youngest family members visit her while she spent summers at Balmoral Castle in Scotland and Christmases at Sandringham, her country estate in Norfolk, England.
The queen was seen pointing things out to her great-grandson, 92 years her junior, and answering his questions as they watched the Trooping the Colour parade from the balcony of Buckingham Palace.