Ofcom received 487 complaints from viewers that the monologue was offensive. It featured Atkinson claiming prayer "doesn't work".
However the regulator stated in July the sketch was not in breach of rules, saying it was justified by the context.
Big Brother, with 965 complaints, was 2013's most complained-about TV show.
It is the second consecutive year the Channel 5 reality show has topped Ofcom's complaints list.
It received complaints across the series concerning a number of issues including racism, bullying and fighting.
1. Big Brother: 965 complaints
2. The X Factor: 734
3. ITV News: 574
4. Comic Relief: Funny for Money: 492
5. Celebrity Big Brother: 438
6. Britain's Got Talent: 422
7. Emmerdale: 376
8. BBC News: 354
9. Downton Abbey: 252
10. Coronation Street: 225
Source: Ofcom - data up to 12 December
The second most-complained about programme was the X Factor results show, which generated 734 complaints.
There were 317 complaints about an episode broadcast in October that featured Lady Gaga performing in an "inappropriate" skimpy outfit made of shells and flesh-coloured underwear.
Ofcom also received 122 complaints over Robin Thicke's performance of Blurred Lines a week earlier, but the regulator ruled there were no grounds to investigate either issue.
ITV News was third on the complaints list, with a total 574 complaints including 278 related to its coverage of the killing of Fusilier Lee Rigby.
An Ofcom investigation into the issue will be published following the conclusion of criminal proceedings. BBC News, 5 News, Channel 4 News and Sky News are also among the broadcasters being investigated for showing graphic pre-watershed images.
Celebrity Big Brother, Britain's Got Talent, Emmerdale, BBC News, Downton Abbey and Coronation Street were also in the top 10 most complained-about programmes.
Ofcom said it had received 13,780 complaints so far this year.
The most complained about programme in the past 10 years was Celebrity Big Brother in 2007, which generated 45,159 complaints after series was rocked by a racism row following remarks by Jade Goody to Bollywood actress Shilpa Shetty.
It meant 2008's series was replaced with Big Brother: Celebrity Hijack.
A Comic Relief sketch starring Rowan Atkinson as a fictional Archbishop of Canterbury is the most complained-about TV moment of the year so far.