Lesley Manville, Lorraine Kelly and comedian Romesh Ranganathan were among others honoured at the London event.
Actor Lennie James was awarded for writing Sky Atlantic's Save Me, which was also named best drama series.
Comer, who plays an assassin in Killing Eve, said her character Villanelle was how "every female role should be".
"To have people come up to me in the street and say they enjoy it is always lovely," she told the BBC's Newsbeat team.
Killing Eve star: Complex female roles are key
Killing Eve was adapted by Fleabag's Phoebe Waller-Bridge from a series of novellas by Observer critic Luke Jennings.
Other winners on Tuesday included Steve Pemberton and Reece Shearsmith, whose work on Inside No. 9 saw them share the male comedy performance award.
The BBC won 15 awards all on what director general Tony Hall said had been "a great night for British creativity".
Originally founded as the Television Society in 1927, the RTS is an educational charity with more than 4,800 members.
It is open to "anyone with an interest in the medium" and not specifically those with links to the industry.
Winners in full
Actor (Female): Jodie Comer - Killing Eve (Sid Gentle Films for BBC One)
Actor (Male): Lucian Msamati - Kiri (The Forge Entertainment for Channel 4)
Arts: The Art of Drumming (Wall to Wall Media for Sky Arts)
Breakthrough Award: Nabhaan Rizwan - Informer (Neal Street Productions for BBC One)
Children's Programme: Prosiect Z (Boom Cymru for S4C)
Comedy Performance (Female): Lesley Manville - Mum (Big Talk Productions in association with The Money Men for BBC Two)
Comedy Performance (Male): Steve Pemberton & Reece Shearsmith - Inside No. 9 (BBC Studios for BBC Two)
Daytime Programme: The Repair Shop (Ricochet for BBC Two)
Documentary Series: Prison (Spring Films for Channel 4)
Drama Series: Save Me (World Productions for Sky Atlantic)
Entertainment: The Last Leg (Open Mike for Channel 4)
Entertainment Performance: Big Narstie and Mo Gilligan - The Big Narstie Show (Exception Entertainment / Dice Productions for Channel 4)
Formatted Popular Factual: The Real Full Monty: Ladies Night (Spun Gold TV for ITV)
History: A Dangerous Dynasty: The House of Assad (72 Films for BBC Two)
Live Event: The Royal Wedding: Prince Harry and Meghan Markle (BBC Studios for BBC One)
Mini-Series: A Very English Scandal (Blueprint Pictures for BBC One)
Presenter: Romesh Ranganathan - The Misadventures of Romesh Ranganathan (Rumpus Media for BBC Two)
RTS Channel of the Year: CBeebies
Science and Natural History: Drowning in Plastic (Raw TV for BBC One)
Scripted Comedy: Derry Girls (Hat Trick Productions for Channel 4)
Single Documentary: Raped: My Story (Lambent Productions for Channel 5)
Single Drama: Killed By My Debt (BBC Studios: The Documentary Unit for BBC Three)
Soap and Continuing Drama: Hollyoaks (Lime Pictures for Channel 4)
Sports Presenter, Commentator or Pundit: Osi Umenyiora - NFL This Week and The NFL Show (Whisper Films for BBC Two)
Sports Programme: MOTD 2018 World Cup: Quarter Final - England v Sweden (BBC Sport for BBC One)
Writer (Comedy): Stefan Golaszewski - Mum (Big Talk Productions in association with The Money Men for BBC Two)
Writer (Drama): Lennie James - Save Me (World Productions for Sky Atlantic)
Outstanding Contribution to British Television: Lorraine Kelly