However he failed to travel to pick up the award, or deliver the lecture that is required to receive the 8m kroner ($910,000) prize.
The academy said it would meet Dylan in private in the Swedish capital, where he is set to perform two concerns, on Saturday and Sunday.
He will not lecture in person but is expected to send a taped version 'at some point'.
If he does not deliver a lecture by June 10, he would have to forfeit the prize money.
Sara Danius, permanent secretary of the Academy, wrote in a blog post: 'The good news is that the Swedish Academy and Bob Dylan have decided to meet this weekend.
'The Academy will then hand over Dylan's Nobel diploma and the Nobel medal, and congratulate him on the Nobel Prize in Literature.
'The setting will be small and intimate, and no media will be present; only Bob Dylan and members of the Academy will attend, all according to Dylan's wishes.'
She added: 'Please note that no Nobel Lecture will be held. The Academy has reason to believe that a taped version will be sent at a later point.'
The rock enigma snubbed the Nobel ceremony on December 10 because of 'pre-existing commitments'.
Nobel laureates usually hold their lectures in Stockholm in the days prior to the ceremony.
Dylan caused some controversy when he took two weeks to officially respond to the honor, prompting members of the Academy to call him 'impolite and arrogant.'
In a bizarre move, his website was updated to acknowledge the win in a description of his book, The Lyrics: 1961-2012, for which he won the prize. But the acknowledgement was taken down the very next day.
He finally officially acknowledged the award on October 28, issuing a statement through the Nobel Foundation.
'The news about the Nobel Prize left me speechless. I appreciate the honor so much,' Dylan said in the statement.
And in a subsequent interview with the Telegraph, Dylan called it an 'amazing' honor to become a Nobel Laureate.
He added: 'It's hard to believe...Whoever dreams about something like that?'
Dylan, who taught himself to play the harmonica, guitar and piano, was also awarded a Pulitzer Prize in 2008 for his contributions to music and American culture.
/Daily Mail/
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