The actress, 82, is the first soap star to receive a best actress nod since Jean Alexander appeared in the category 20 years ago for her role as Hilda Ogden in Coronation Street.
She will battle Anna Maxwell Martin (Poppy Shakespeare), Andrea Riseborough (The Long Walk to Finchley) and Maxine Peake (Hancock and Joan) for the award.
Brown was nominated for the gong for her ground-breaking solo episode of the BBC soap, where her character Dot Cotton bid farewell to on-screen husband Jim Branning (John Bardon).
"This is a fantastic moment for June, made all the more special by the quality of the other nominees," said Santer.
"Traditionally it has been almost impossible for our actors to break through into these kinds of awards. June is a truly remarkable and unique talent."
Speaking about her nomination, Brown said: "It was a lovely episode to film, thanks to our fantastic director Clive Arnold and wonderful crew. I was very fortunate to be given the opportunity."
EastEnders is also nominated for best continuing drama at the ceremony, which takes place on April 26.