The popular star picked up the title for the second year running for her role in Broadchurch with judges calling her "an actor at the top of her game".
Taking to the stage shoeless, she said: "I kicked them off under the table and forgot to put them back on."
Broadchurch won a second prize at the London event hosted by comic Tim Vine by landing the best drama serial award.
Idris Elba took the best actor prize for his performance in BBC One detective series Luther.
Other winners included ITV's Corornation Street, which took the prize for best soap and Stephen Fry who was named best presenter for his series Stephen Fry: Out There in which he travelled to a number of countries to examine how they treated their gay communities.
The broadcaster famously made an attempt on his own life as he made the series as it left him at such a low ebb. He paraphrased Winston Churchill to tell guests at the ceremony: "I think you can judge a civilisation by the way it treats its minorities."
Channel 4 was the biggest winner of the night sharing in nine awards for which it was the broadcaster, including the best documentary series prize, which went to Educating Yorkshire. Maths teacher Michael Steer from the show blasted Education Secretary Michael Gove as he collected the gong.
Outgoing BBC Two controller Janice Hadlow was given the "judges' award" for her achievements with the channel.
Veteran actor David Suchet was honoured with the lifetime achievement award in recognition of his quarter of a century portraying Hercule Poirot.
The star was unable to attend the event after feeling unwell before the ceremony.
The winners of the RTS Programme Awards were:
Olivia Colman - Broadchurch (ITV)/Run (Channel 4)
Idris Elba - Luther (BBC One)
Imagine...Vivian Maier: Who Took Nanny's Pictures (BBC One)
Dumping Ground (CBBC)
Hard Times - A Newsround Special (CBBC)
Brendan O'Carroll - Mrs Brown's Boys (BBC One)
Four Rooms (Channel 4)
Educating Yorkshire (Channel 4)
Peaky Blinders (BBC Two)
The Last Leg (Channel 4)
Alan Carr - Alan Carr: Chatty Man (Channel 4)
Richard III: King In The Car Park (Channel 4)
Game Of Thrones (Sky Atlantic)
The Ashes - 2013 (Sky Sports)
Popular, Factual and Features
Gogglebox (Channel 4)
Stephen Fry - Stephen Fry: Out There (BBC Two)
Science and Natural History
Africa (BBC One)
The Murder Trial (Channel 4)
The Challenger (BBC Two)
Soap and Continuing Drama
Coronation Street (ITV)
Sports Presenter, Commentator or Pundit
Gary Neville - Sky Sports (Sky Sports)
World Athletics - Mo Farah's Double Gold Win (BBC One)
James Corden, Mathew Baynton and Tom Basden - The Wrong Mans (BBC Two)
Marlon Smith and Daniel Fajemisin-Duncan - Run (Channel 4)