A total of 36,262 votes were cast online to choose the cover from a shortlist of the top 10 compiled by a panel of experts, to celebrate the PPA’s centenary this year.
The Radio Times Dalek cover beat rivals including an Empire cover starting Darth Vadar from 'Star Wars', and a Woman’s Weekly cover from 1916.
‘Vote Dalek’ was released to mark the return of the return of the extra-terrestrial villains to the BBC show after two decades, and also coincided with the 2005 general election.
The runner-up was The Beano's 'Dennis The Menace' cover, which celebrated the cartoon magazine's 75th birthday in February 1999. The issue marked the first time that its character Dennis appeared in non-comic-strip style.
In third place was Time Out's November 1974 cover, featuring two fingers stuck up in a "V" shape, to explore a different side of former Prime Minister Winston Churchill on what would have been his 100th birthday.
Tom Bureau, chief executive of Radio Times publisher Immediate Media, said: "It's a huge honour for Radio Times to have been voted cover of the century by the great British public.
"Radio Times and 'Dr Who' are both iconic media brands that continue to go from strength to strength with regeneration at the heart of their success. This award exemplifies what the Radio Times brand does best – creating national conversations around the key moments in broadcasting history."
The top 10 covers were:
Woman’s Weekly: ‘Wartime Women’, July 1916
Harper’s Bazaar: ‘Fashion Blitz’, November 1941
Cosmopolitan: launch issue, March 1972
Time Out: ‘Churchill V-Sign’, November 1974
New Scientist: ‘Chernobyl’, April 1987
The Beano: ‘Dennis The Menace’, February 1999
Vogue: ‘A Royal Salute’, December 2001
Radio Times: ‘Vote Dalek!’, April 2005
Empire: ‘Breathing Vader’, June 2005
MacUser: ‘How Evil is Apple?’, February 2012
The cover announcement coincided with the PPA’s centenary celebrations, which culminated in a gala dinner last night at the Park Lane Hotel.
The association has published a 132-page 'PPA 100' magazine, to mark its centenary year, edited by Gill Hudson, ex-editor of Reader’s Digest, Radio Times, Company and Maxim.
It includes comment on the future of the industry by from the leaders such as Nicholas Coleridge of Condé Nast and Kevin Costello of Haymarket Media Group, a look at the PPA’s history and '100 great magazine moments', such as Margaret Thatcher’s controversial interview with Women’s Own in 1987.Follow @LouiseRidley