Digital Spy caught up with Moffat on the eve of this announcement to discuss his accolade, his two hit shows and his plans for the future...
How does it feel to win this BAFTA Special Award?
"Well, I don't know, it's a bit like being shown your mausoleum! No, it's great, it's really exciting, of course. It fends off the insecurity for 10 or 15 minutes more a day, I suppose! It's absolutely lovely, absolutely thrilling."
You've had a varied career - do you take a different approach to writing something like Doctor Who than you did with Coupling or Joking Apart?
"It may look as though I take a different approach, but I don't think any writer ever does. I think you just write it, with the same anxieties - you want it to be interesting, you want it to be funny and full of incident... I don't think there is a different way to write. Just keep being interesting, keep people from turning over...
"Writing a comedy, you're doing that exclusively more or less with jokes. If you're doing a drama, you've got a wider palate, as it were. You've got a broader range of things you can do - it can be exciting moments or surprising twists. But really and truly, all you're ever doing is imagining someone reaching for the remote and trying to stop them!"
Is series three of Sherlock now in the planning stages?
"Well, we've had meetings about it. It's certainly happening and we know when we're filming it - we shoot in January. Obviously I've got quite a lot of work on between now and January!
"So yes, it's all happening and we've had our first few meetings. I don't think a word has been committed to paper yet, but nearly."
Have you decided which Conan Doyle stories you're going to adapt this time?
"Yes - and that's not to say that it won't change at all as it goes along, because it always does. But broadly speaking, yes, we have our arc and we know what we're going to cover. The writing depends to some degree on spontaneity so you give yourself a big enough framework to improvise within."
Presumably The Adventure of the Empty House will be the first episode?
"Well, there will be the return, let's put it that way!"
And it'll be yourself, Mark Gatiss and Steve Thompson writing the three episodes again?
"That's right, yes."
You've talked in the past about the new CBS Sherlock Holmes series Elementary - have you had a chance to check out the trailer?
"To be honest, I think my quotes on [that show] have been rather exaggerated. Someone asked me what I thought about making Watson a woman and I said, 'I wonder how many things you could change before it isn't Sherlock Holmes anymore?'.
"But I don't know - I haven't seen it, so I can't really comment on that sort of thing. I think everyone's very anxious for me to have a go at it, and I'm really not."
When we spoke to Gina Bellman, she suggested that your 2007 drama Jekyll could've been as big as Sherlock has become - do you agree with that?
"It didn't hit its moment, but I thought it was great. I was thrilled with Jekyll - generally speaking, it got very good reviews. I don't know what the alchemy is when something absolutely hits the way Sherlock did. I think it's a combination of... it's a good show and all that, but it was the right moment somehow. Sometimes that just happens.
"It didn't happen for Jekyll - the performance was perfectly respectable, it has to be said. There was nothing wrong with it, it just wasn't a breakthrough show. Whereas Sherlock instantly struck a chord.
"Before anyone had even seen it, it was a hit, because people turned up for its first broadcast - they couldn't have known if they were going to like it. So it was just one of those things - we must have hit exactly the right moment to do that with Sherlock Holmes."
They're similar shows in the sense that they're updates of a familiar brand...
"I think Sherlock Holmes is the bigger brand, let's be honest. But whether or not that's an advantage is interesting, oddly enough, because there have been many, many Sherlock Holmes [adaptations] that have failed. So I don't know if that hugely helps us.
"They're similar in that they're updates of famous Victorian stories, but once you get past that, I don't think they're that similar - Jekyll was obviously a sequel, Sherlock is just a straightforward update. They didn't feel similar to write."
Moving on to Doctor Who - how was it bidding farewell to Karen Gillan (Amy) and Arthur Darvill (Rory)?
"Oh, it's incredibly sad. The thing you can forget about this is, while the audience are losing people that they see for a few months per year, Karen and Arthur are walking out of something that they've been involved with every day for years. It's not just a professional change, it is a personal upheaval.
"I'm trying not to say it's like being dumped, but a huge part of your life changes. I think of Karen and Arthur, and from Matt [Smith]'s point of view - people that you saw every single day and have become absolutely part of your de facto family are now gone, never ever to be in that place in your life again.
"So it's a huge upheaval - it's personal and it's human. People should not underestimate how upsetting it is for everybody involved in it. I don't mean 'upsetting' in the sense that it's a tragedy - it's not a tragedy! But it's a huge bloody change - it's someone moving out of your house, that's how big it is."
There are going to be five Doctor Who episodes in the autumn, then a Christmas special, then eight more in 2013 - what was the thinking behind that structure?
"I don't know, on this occasion, that the thinking particularly came from me, actually. I've always been open to anything that shakes [the series] up. I think that decision actually came from the BBC.
"But I've been well up for anything that we can do to shake up the transmission pattern, the way we deliver it to the audience and how long we make the audience wait, simply because that makes Doctor Who an event piece.
"The more Doctor Who becomes a perennial, the faster it starts to die. You've got to shake it up, you've got to keep people on edge and wondering when it will come back.
"Sherlock is the prime example, as far as that goes. Sherlock almost exists on starving its audience. By the time it came back this year, Sherlock was like a rock star re-entering the building!
"So keeping Doctor Who as an event, and never making people feel, 'Oh, it's lovely, reliable old Doctor Who - it'll be on about this time, at that time of year'. Once you start to do that, just slowly, it becomes like any much-loved ornament in your house - ultimately invisible. And I don't want that to ever be the case."
"Christmas! But don't expect to learn everything! We've got a good story and there are some proper legitimate surprises in it. I'm excited by it. I think we're going to do some fun stuff."
Are you hoping to conceal the companion's identity until the Christmas special actually airs?
"We can't really contain everything, because people will crawl all over us with cameras and sneak views of scripts and call-sheets. Something will get out. But we've been fairly sly, so let's wait and see.
"Again, a lot of the audience that I talk to specifically avoid any spoilers and I'm absolutely certain they have a better experience of the show. As I've always said, if I could make it on the dark side of the moon, I would, but you can't do these things.
"i got pilloried by somebody at some deep level of naivety about the industry - they were angry that I'd revealed the fact that Amy and Rory were even going to leave! But y'know, actor's agents really do have to advertise their client's availability - I had no choice but to announce they were going to leave. But in an ideal world, you wouldn't even do that."
And are plans for the 50th anniversary of Doctor Who under way too?
"Yes, they are. I had a meeting about that earlier in the week!"
The Arqiva British Academy Television Awards 2012 take place at the Royal Festival Hall at London's South Bank centre on Sunday, May 27 and will be broadcast on BBC One.