Lambeth Palace said Justin Welby will not be preaching at St Paul’s Cathedral in London for the celebration later this week.
The archbishop said he was “deeply saddened” to be missing the service marking 70 years on the throne for Queen Elizabeth II.
The 66-year-old has been suffering from mild pneumonia since last week, according to Lambeth Palace.
It said he developed Covid symptoms over the weekend and did a positive test on Monday.
He was due to preach at the Service of Thanksgiving for the longest reigning British monarch on Friday, when St Paul’s church bell – the largest in the country – will be rung for the first royal occasion in its history.
The Archbishop of York, Stephen Cottrell, will preach the sermon instead.
In a statement on Monday, Welby said: “I am deeply saddened to be missing the historic celebration of Her Majesty the Queen’s Platinum Jubilee.
“However, I will be praying for the Queen and giving thanks for her extraordinary seventy years of service to us all.”
He added: “For those attending Friday’s service at St Paul’s Cathedral, and the millions watching on television, I hope this joyful occasion will inspire us with the Queen’s profound commitment to fostering unity and peace among all people – and to promoting care for the natural world that God has given us.”
Lambeth Palace said the Archbishop has cancelled all engagements for the week as he rests at home and avoids contact with others in keeping with both medical advice and national Covid guidance.
He will also not be able to light a beacon at Lambeth Palace on Thursday as planned for Jubilee celebrations – but this will still be lit on his behalf.
Festivities are set to kick off on Thursday for the Platinum Jubilee, which is the first in British history.
The four days of celebrations are set to include a military spectacle, a visit from Harry and Meghan and live performances at the BBC’s Party at the Palace.