The Royal Family were presented with flowers
The 101-year-old was absent as a number of other royals including the Countess of Wessex attended church on the Queen's Norfolk estate.
The BBC's royal correspondent Nicholas Witchell said the Queen Mother was suffering from a cold, and it was a particularly cold Christmas morning at Sandringham.
The Countess of Wessex arrived by car with the Queen.
It was Sophie's first public appearance since undergoing emergency surgery for an ectopic pregnancy earlier this month.
She has been convalescing at her home, Bagshot Park in Surrey, since leaving hospital on 10 December following the operation.
Observers said she looked pale as she arrived at the service, which was also attended by her husband, the Earl of Wessex.
But after the service the couple chatted and laughed with Canon George Hall and relatives outside the Church of St Mary Magdalen.
Sophie was then helped down the steps to the Queen's limousine by Prince Edward and the Princess Royal's husband, Commodore Timothy Laurence.
Other royals who took part in the traditional Christmas Day celebrations included Prince Charles and his sons princes William and Harry, and Prince Andrew and his daughters princesses Beatrice and Eugenie.
Queen's speech
During the service, which was relayed by loudspeakers to the 1,000-strong crowd outside, Canon Hall urged the congregation to remember both the Queen Mother and Princess Margaret in their prayers.
Princess Margaret, 71, who suffered three suspected strokes in 1998 and in January and March of this year, was also not well enough to attend.
The Queen Mother underwent hospital tests in September, after having a blood transfusion for anaemia in August.
She failed to make her customary appearance at Scotland's most famous Highland games, the Braemar Gathering, at the end of August.
But since then she has made several public appearances, including a re-dedication ceremony to celebrate HMS Ark Royal going back to sea last month following a £147m refit.
Both the Queen Mother and Princess Margaret are at Sandringham House, and a Buckingham Palace spokeswoman said they were "both joining in the Royal Family's Christmas celebrations".
Many of the royals who did gather for the 40-minute service chatted to well-wishers afterwards, and received flowers, cards and other Christmas gifts.
Prince William, 19, was presented with a bag Hershey's Kisses - American chocolates - from a six-year-old admirer.
Katherine Bennett, whose father is an American army surgeon based at RAF Lakenheath, Suffolk, chased after the prince to give him her gift and wish him a merry Christmas.
Later on Tuesday, the Queen appeared on television, radio and the internet, delivering her annual Christmas message, recorded at Buckingham Palace.
Proposals to send a version by text message to mobile phone users next year are being considered by the palace.
Centenarian
Prime Minister Tony Blair also sent his annual Christmas message to the British service men and women who are on duty at home and abroad this Christmas.
His speech was transmitted on British Forces Broadcasting Service (BFBS) and was heard by soldiers all over the world.
The Queen's aunt, Princess Alice, is celebrating her 100th birthday on Christmas Day.
The dowager Duchess of Gloucester received a congratulatory "telegram" from the Queen as she joins the Queen Mother as the Royal Family's second centenarian.
A 100th birthday party was thrown for her at her Kensington Palace home earlier this month.