James Bond and Paddington star Whishaw collected best actor for his performance as an under pressure doctor in BBC series This Is Going To Hurt.
Anne-Marie Duff won supporting actress for her portrayal of Grace Williams in Bad Sisters, which also won best Drama Series.
Adeel Akhtar won the BAFTA for supporting actor for his role in the crime drama Sherwood.
Bad Sisters, Derry Girls, I Am Ruth and The Traitors also took home two BAFTAs a piece at the event, held at the Royal Festival Hall on Sunday.
Meanwhile, Platinum Jubilee - Party at the Palace: Paddington meets the Queen, was the winner of the P&O Cruises Memorable Moment Award - the only gong voted for by the public.
Winslet took home the last award of the night - best actress. Winslet’s daughter Mia Threapleton played her on-screen daughter in the show.
In an emotional speech, the Titanic star said: “If I could break it in half, I would give the other half to my daughter, we did this together, kiddo.”
I Am Ruth also won single drama.
Meanwhile, accepting his award Whishaw, 42, said: “I’m very humbled, and blessed.”
The medical drama is based on Adam Kay’s book which chronicles his work training to be a doctor in the NHS.
It was also the second time Whishaw had appeared on stage to collect the prize for most memorable moment for his sketch as Paddington Bear featuring the late Queen in honour of her Platinum Jubilee celebrations.
The night also saw Sir Mo Farah win a Bafta award for his BBC One documentary The Real Mo Farah which revealed he had been illegally trafficked to the UK as a child.
Collecting the best single documentary prize, the four-time Olympic champion dedicated the award to “children who are being trafficked”.
In his speech, he said: “The kids have no say at all, they are just kids and no child should ever go through what I did, I hope my story shows they aren’t alone, we are in it together.”
The 40-year-old thanked the team at the BBC because it “wasn’t easy” to film and he wouldn’t have been able to it “without them”, while his wife Tania Nell said it was the couples children who “empowered” them to tell the story.
Other poignant speeches came from best supporting actress Duff for the comedy Bad Sisters, who said that TV is a “political arena” and shared a message to people at home.
The 52-year-old Sex Education star said: “If someone..is in their life who is bullying them who is telling them that who they are is wrong, that what they are isn’t enough…I am telling you now you are everything.”
It was also a big night for entertainment programmes, as ITV’s The Masked Singer fought off competition from Ant And Dec’s Saturday Night Takeaway and Strictly Come Dancing to win best entertainment programme.
Host Joel Dommett joked in his speech: “I really didn’t expect this, Strictly normally wins everything.
“Thank you so much to ITV firstly for believing in this silly show, it is so silly and it’s so wonderful, it has brightened up so many families and homes.”
Meanwhile, the reality and constructed factual award went to hit BBC One psychological adventure show The Traitors which sees strangers play “the ultimate game of detection, backstabbing and trust” at a Scottish Highlands castle in the hope of winning big.
Host Claudia Winkleman, 51, later picked up the Bafta for entertainment performance for the series, saying she didn’t want to get emotional as her mascara “will run” before asking her husband: “Please, can we have a dog?”
She also “thanked” her mother and father and said it was “for you” before saying: “You can’t have it… no, but you can touch it.”
The Uefa Women’s Euro 2022 coverage also won a Bafta TV award for best sports coverage, after the Lionesses became the first England football team to win an international tournament since 1966.
Meanwhile Channel 4 News: Live In Kyiv won a Bafta TV award for best news coverage, beating Susanna Reid’s Good Morning Britain interview with then prime minister Boris Johnson.
Lewis Capaldi gave his first televised performance of new single Wish You The Best alongside DJ Jax Jones and singer Calum Scott who took to the stage performing their song, Whistle.
Jones said: “Big up Kate Winslet” ahead of performing the track which also saw dancers dressed as fish on stage.