Windsor won the award for her role in Three Girls, a drama about three victims of the Rochdale child sex abuse scandal.
Collecting the prize from Sherlock star Martin Freeman, she said: “Three Girls was born out of the courage of the real three girls, and the real Holly, Amber and Ruby who told their story over and over and over and told it again to us.
“I just want to say thank you for recognising how selfless that is and how brave that is.”
The drama also won the prize for best mini-series.
Writer Nicole Taylor dedicated the prize to health worker Sara Rowbotham and former detective Maggie Oliver, who helped blow the whistle on the scandal, as well as the real three victims and their families.
Foy had been nominated for a second consecutive year for her role as the Queen in The Crown, while Newton was nominated for her part in Line Of Duty.
Foy, who sported a Time’s Up pin on her white dress, spoke about her support for the campaign ahead of the ceremony, saying: “It’s about not thinking this is just a moment.
“It’s not a moment, it’s a continuing evolving thing and in five or six years’ time we’ll know how much progress we’ve made, and I think it’s just a really important thing to support.”
Sean Bean was named best leading actor for his role as a Roman Catholic priest in Broken.
BBC Three’s This Country, a mockumentary which depicts life in rural Britain, won two awards.
It received the BAFTA for scripted comedy, while writer and star Daisy May Cooper won female performance in a comedy programme.
Former footballer Rio Ferdinand won best single documentary for Being Mum And Dad, a film about the loss of his wife Rebecca to cancer.
“It’s been quite a crazy whirlwind experience,” he said on accepting his award.
“I didn’t do this for any other reason than my three kids.
“The worst thing to come out of this is I get quite emotional now but it’s allowed me to speak and show vulnerability that people aren’t used to because as a sportsman you’re built up to be indestructible.”
He said the documentary had helped him heal and referring to his “beautiful girlfriend” Kate Wright, he said: “We are making steps in the right direction”.
Sky News also won an award for its coverage of the Rohingya crisis.
Meanwhile, the highest accolade the Academy bestows, the fellowship, was presented to journalist Kate Adie.
Speaking about the importance of reporting, she said: “It’s essential in a democracy, we tell truth to power.
“We tell it like it is and in these times that is more important than ever.”
Britain’s Got Talent won the BAFTA for best entertainment programme, with judge Amanda Holden saying Ant McPartlin would be missed during upcoming live shows.
Holden said: “I think he will be missed but Dec will do a sterling job and Alesha and I are on hand to step in!
“I think Mand and Dec has a nice ring to it!”
ITV confirmed Dec would be hosting the live shows without his TV partner of almost 30 years after Ant was given a fine and a ban for drink-driving.
BAFTA TV Award winners:
Molly Windsor (Three Girls)
Sean Bean (Broken)
Brian F. O’Byrne (Little Boy Blue)
Vanessa Kirby (The Crown)
Murdered For Being Different
Soap & Continuing Drama
Britain’s Got Talent
Comedy Entertainment Programme
Murder in Successville
BAFTA for Reality & Constructed Factual
The Handmaid’s Tale
Cruising with Jane McDonald
Short Form Programme
Morgana Robinson’s Summer
Sky News’ The Rohingya Crisis
Undercover: Britain’s Immigration Secrets (Panorama)
Rio Ferdinand: Being Mum And Dad
Basquiat – Rage To Riches
Female Performance in a Comedy Programme
Daisy May Cooper (This Country)
Male Performance in a Comedy Programme
Toby Jones (Detectorists)
The Grand National
World War One Remembered: Passchendaele
The Special Award
John Motson OBE
Kate Adie OBE
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