ITV's 'The Bill', BBC's 'Holby City' and BBC daytime soap 'Doctors' also made the Best Continuing Drama shortlist.
BBC bosses were hoping to put an end to a troubled year including the soap's worst ratings in its 20-year history, down to 6.3m viewers, script rewrites and Leslie Grantham's finger-sucking internet scandal.
But despite appealing to academy chiefs to be included in this year's nominations, 'EastEnders' was left out in the cold.
It was not bad news for the corporation alone, with ITV's 'Emmerdale' not receiving a nomination despite having attracted some of its best ratings and most explosive storylines in the past year. 'Coronation Street' is expected to retain the award on April 17.
Other Bafta nominations include:
Best Sitcom:
'Green Wing', Channel 4
'Black Books', Channel 4
'Nighty Night', BBC Three
'The Vicar of Dibley Christmas Special', BBC One
Best Comedy Performance:
Matt Lucas and David Walliams: 'Little Britain', BBC Three
Rory Bremner: 'Bremner, Bird and Fortune', Channel 4
Julia Davis: 'Nighty Night', BBC Three
Tamsin Greig: 'Green Wing', Channel 4
Best Entertainment Performance:
Ant and Dec: 'I'm a Celebrity... Get Me Out of Here!', ITV
Stephen Fry: 'QI', BBC Two
Paul Merton: 'Have I Got News For You', BBC One
Paul O'Grady: 'Paul O'Grady Show', ITV
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