The American architect is the eighth winner of the Women in Architecture award, founded by the Architectural Review and the Architects Journal (AJ).
AJ editor Emily Booth said Diller, who was recently named one of Time magazine's most influential people, is an "international architectural powerhouse".
"From her wide range of work – including the High Line in New York, to The Broad art museum in Los Angeles, to the much-anticipated London Centre for Music – Diller's brave, refreshing, innovative and often cross-disciplinary approach is an inspiration to the architectural profession," Booth added.
Diller Scofidio + Renfro unveiled designs for a landmark building in London last week, a pyramidal tower that will house a new concert hall for the Barbican.
In New York they have completed an 88-storey skyscraper and are currently building an eight-storey cultural centre called the Shed, which features an extendable roof that can move forward on rails to cover an adjoining plaza.
Diller Scofidio + Renfro's The Shed has a moving roof that doubles the building's size
Diller said she was "very touched" to be the recipient of the 2019 Jane Drew Prize, and honoured to join the ranks of the "amazing group of women that came before."
After her inclusion on Time's power list, Diller said that the architecture industry was finally beginning to make strides towards gender equality, helped by initiatives including International Women's Day and movements targeting harassment such as #MeToo.
"Architecture has been male-dominated forever and I am a grateful beneficiary of the women's movement," Diller told Dezeen.
"It's a sign of a dramatic change in the profile of what an architect looks like."
Women architects around the world have been fighting to change perceptions of what makes a successful architect in an industry where leaders are often overwhelmingly male.
In Mexico female architects are blazing the trail for women-led practices eschewing a male partner.
Meanwhile Italy's national institute of architects caused a huge scandal by failing to recognise Italian architect Doriana Fuksas, only awarding the Premio alla Carriera Architettura prize to her male partner.