Avalanna Routh was dubbed 'Mrs Bieber' by her friends and family.
Routh's family wrote on Twitter: "Our darling Avalanna went to Heaven this morning. Oh Avalanna, the brightest star - you took our hearts with you, our greatest love."
Bieber also made a statement on the micro-blogging website which read: "Just got the worst news ever. One of the greatest spirits I have ever known is gone. Please pray for her family and for her. RIP Avalanna. I love you."
Sharing a picture of the two of them together, the singer added: "Please show respect to her and her family. Say a prayer for her and for them. I miss her."
Bieber had paid Routh a visit earlier this year in New York, after a family friend created a Facebook petition titled "Get Avalanna to Meet Justin Bieber."
They also made a joint appearance on the Today show in June.
After meeting Routh for the first time, Bieber told fans that it was "one of the best things I have ever done. She was AWESOME! Feeling really inspired now #MrsBieber."
Routh was diagnosed with a rare and aggressive cancer at 9 months old called an AT/RT, or an atypical teratoid/rhabdoid tumor. Most of those diagnosed with the ailment are given a maximum of a year to live, and there is currently no known cure.
Dr Charles Roberts, a paediatric oncologist at the Dana-Farber Children's Hospital Cancer Centre, told the Los Angeles Times that AT/RT is "a cancer that strikes babies and toddlers and arises in the brain... We are still having an extremely difficult time curing this type of cancer."
Staff at the hospital threw a fake wedding for Routh that included flowers, a wedding cake and a singer. They also gave her a red T-shirt that read 'Future Mrs Bieber'.
Roberts said that Routh's passing had devastated staff, adding: "People are taking it very hard. We knew it was coming, but it's extremely sad."
Watch Justin Bieber and Avalanna Routh together on the Today show below: