The episode, which went out on Sunday night, has seen complaints from fans.
Fellowes told The BBC that the plot had been handled sensitively: "The whole point of the way we do things on Downton is we don't do them gratuitously," he insisted.
"We are interested in exploring the resultant emotions and the effect these things have on people."
But he apologised to fans, saying he was "sorry" if they felt the show couldn't "go there".
Stressing that the attack took place behind closed doors, he added: "If we'd wanted a sensational rape we could have stayed down in the kitchen with the camera during the whole thing and wrung it out.
"We're interested in exploring the mental damage and the emotional damage."
Since the show, both actors involved in the scenes, Nigel Harman and Joanne Froggatt, have supported the story in interviews.
Early today Froggatt said: "I was really proud of the show for tackling a subject like this. It's a really brave thing to do and I really do believe that Julian's written that in a way that is not gratuitous at all, he does very much go on to explore the emotional journey of Anna and Bates.
"He's done a beautiful job of hitting the right note with it. I think we all just felt a big responsibility to get it right," she said in an interview on BBC Breakfast.
On Monday, Nigel Harman told This Morning that the story was exciting yet risky: "Because for a show like Downton it really leaped out as a bold and risky idea... and I'd worked with Joanne Froggatt and Brendan Cole before and we had a rehearsal and went for it. And what we wanted to do was to try and not signal about what was to come."
Fellowes, who wrote Oscar-winning film Gosford Park in 2002, said the plot development did not signal a new direction for the drama series, now in its fourth run.
"Downton deals in subjecting a couple of characters per series to a very difficult situation and you get the emotions that come out of these traumas. All of this is about taking characters to the brink. We know Anna is a strong personality but it doesn't mean she will be able to be strong through this."