The lavish Netflix series, starring Claire Foy as the Queen, left empty-handed despite going into the awards with five nominations.
Gritty BBC1 drama Happy Valley and its star Sarah Lancashire triumphed over its royal rival in the best drama series and leading actress categories, while The Crown also missed out on gongs for supporting actor and actress.
Screenwriter Emma Frost wrote on Twitter: "I've been on Bafta TV juries so know each is separate and independent. But for The Crown to win nothing? Feels a deliberate snub to Netflix."
@MagicTorch82 wrote: "How is it possible The Crown did not win any Bafta awards? Speechless. Now, if it was a BBC show I'm sure it would be a different story."
@TheKayeCrawford wrote: "Shameful that The Crown hasn't been recognised by Bafta. Snobbishness that it was produced by Netflix one wonders? Very mean."
But @Holly_Drummond wrote: "Attempted to watch The Crown on Netflix. Couldn't get into it at all."
And @baggottsilver added: "The Â£100 million Netflix spent on The Crown looking like quite a lot of money now... Well done Happy Valley."
In a night of success for the BBC, other wins as well as Happy Valley included Charlie Brooker's 2016 Wipe, Michael McIntyre's Big Show, Who Do You Think You Are?, Fleabag's Phoebe Waller-Bridge, drama Damilola, Our Loved Boy, The Night Manager's Tom Hollander, reality series Muslims Like Us, and Planet Earth II.
Director of BBC content Charlotte Moore called the triumphs "an incredible night for the BBC".
"I want to thank all the winners for their contribution to British television - the sheer quality on display is inspiring, and I feel honoured to lead BBC content on such top creative form," she said.