The BBC1 serial was also beaten by arch-rival Coronation Street with the ITV show taking the honours as the top festive soap opera for the first time in more than a decade.
Mrs Brown's Boys - the bawdy BBC Scotland show created by Irish comic Brendan O'Carroll, which has become a surprise ratings hit - pulled in an average audience of 9.4 million.
Corrie tied with Doctor Who - which included Matt Smith's regeneration into the new doctor Peter Capaldi - on 8.3 million viewers, to jointly claim second spot in the viewing league table.
The Dr Who special, which saw The Doctor age 300 years and included a brief return for Karen Gillan as Amy Pond, was up 700,000 viewers on last year.
This year's figures will be seen as a setback for EastEnders, which used to regularly top the Christmas viewing figures. This year's episode was packed with incident, including the arrest of Janine Butcher for murder and the arrival of new Queen Vic landlord Mick Carter - played by Danny Dyer. The show lost 1.6 million viewers compared with last year.
The BBC took six of the top ten places, but the Queen's Christmas broadcast missed out at the top end of the list. BBC1's audience for the annual address traditionally figures in the top ten but this year's 5.7 million meant it failed to figure in the top shows.
However, with the 2.1 million who watched on ITV, the broadcast managed a combined 7.8 million.
The BBC News lost its place in this year's top ten, replaced by the ITV News.
BBC1 controller Charlotte Moore said: "Nothing brings the country together at Christmas quite like BBC1. Huge audiences shared the Christmas Day schedule on the nation's favourite channel winning 4 out of the top 5 most popular shows.
"Mrs Brown's Boys took the top spot with 9.4 million viewers, and the arrival of Peter Capaldi created the biggest peak audience at 10.2 million in Doctor Who."
1. Mrs Brown's Boys BBC1, 9.30pm) - 9.4m
2= Doctor Who ( BBC1, 7.30pm) - 8.3m
2= Coronation Street ( ITV, 7.30pm) - 8.3m
4. EastEnders (BBC1, 8.30pm) - 7.8m
5. Strictly Come Dancing (BBC1, 5pm) - 7.3m
6. Call the Midwife (BBC1, 6.15pm) - 7.1m
7. Downton Abbey (ITV, 8.30 pm) - 7m
8. Toy Story 3 (BBC1, 3pm) - 6.3m
9. ITV News (ITV, 10.30pm) - 5.9m
10. Emmerdale (ITV, 6.15pm) - 5.8m
All ITV figures in the overnight ratings include viewers on the catch-up plus one service.