She was 98 and is survived by son Sandip Ray who is a well-known Bengali film director.
Long suffering from a lung-related illness, Bijoya was admitted to super-speciality hospital Belle Vue clinic last evening with acute pneumonia.
After her condition deteriorated, she was put on ventilation support.
"Doctors tried their best to save her life, but she passed away at around 6 pm," Belle Vue CEO Dr P Tandon told PTI.
Born in 1917, Bijoya got married on October 20, 1948.
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She had acted in a few films and had penned her days with her famous husband in an autobiography 'Amader Katha' which was later translated into English as 'Manik and I'.
Hearing the news, West Bengal Chief Minister Mamata Banerjee went to the hospital and offered her condolence to the bereaved family.
Describing Bijoya as a bridge between two generations of film-makers - Satyajit and son Sandip - she said that her demise was an irreparable loss not only to the Ray family, but all of them.
"Other than films, Bijoya Ray had a special interest for western classical music. Her demise is an irreparable loss not only to the Ray family, but all of us. I convey my sympathies to the bereaved family and pray that her soul rest in peace," said Banerjee in a message.