Daniel - sporting hair extensions for his role as Igor in the new adaptation of Frankenstein - was crowned Best Actor in a Play for his performance in The Cripple of Inishmaan. Rupert, meanwhile, took home the Newcomer of the Year award for his West End debut in Jez Butterworth’s Mojo, playing a 1950s drug dealer.
It was the second time Daniel has been awarded a WhatsOnStage trophy – he won Rupert's prize in 2008 for his role in Equus.
"I am deeply honoured to receive this prestigious award and I accept it on behalf of the whole cast who together helped make this production… a truly joyous experience for me as an actor," 24-year-old Daniel said as he accepted the accolade for his role in the black comedy, about a bullied disabled man with dreams of stardom.
The winners of the WhatsOnStage awards are voted for by the public, and the Harry Potter stars have clearly captivated both theatre-goers and critics alike.
Daniel on stage at the awards
Dame Helen Mirren was also honoured on the night, named Best Actress in a Play for her role as Queen Elizabeth II in The Audience. In a pre-recorded speech, the star – recently honoured with a BAFTA fellowship – said, "I'm so thrilled to receive this. I'm honoured that it was voted for by the public, that's the most wonderful thing."
David Walliams received the Best Supporting Actor in a Play for his work in A Midsummer Night's Dream, which also won Best Shakespearean Production.
David Walliams also picked up an award
The Book of Mormon took home four awards: Best New Musical, Best Actor in a Musical for Gavin Creel, Best Supporting Actor in a Musical for Stephen Ashfield and Best Supporting Actress in a Musical for Alexia Khadime.
Mathilda the Musical won Best West End Show, and Barry Humphries – best known as his alter ego Dame Edna Everage - picked up the Best Solo Performance for his farewell tour Eat Pray Laugh!.