The service at King’s College in Cambridge is pre-recorded each year and broadcast on BBC Two on Christmas Eve, marking the start of Christmas for many.
Two adult choral scholars, within the same household, tested positive for coronavirus and are in precautionary self-isolation, the college said.
They suffered only mild symptoms.
Internationally renowned vocal group The King’s Singers were asked to step in to join the young choristers at 48 hours’ notice.
The two groups, which stood a safe distance apart, sang with each other for the first time just minutes before filming of this year’s Carols From King’s service began.
Filming was completed on Sunday evening.
Revd Dr Stephen Cherry, Dean of King’s College, said: “We are all hugely grateful to The King’s Singers for stepping up at the last minute.
“They have shown tremendous goodwill and consummate professionalism.
“Our young choristers also responded very positively and with real maturity to the several challenges faced in reimagining the programme, and together they have enabled us to offer a wonderful Christmas service at extraordinarily short notice.
“King’s College Choir has been preparing for our Christmas broadcasts for months while following strict safety protocols, so it was particularly disappointing that the choral scholars couldn’t be with us for the filming.
“To have had one of the households hit by the virus at the last moment was incredibly unfortunate.
“In a year when so many will be spending Christmas in a way unlike any other in living memory, we were determined to do whatever we could to offer a meaningful and beautiful Christmas service.
“We’re delighted with the result of the remarkable efforts of so many people at King’s and at the BBC, and we look forward to sharing Carols From King’s with viewers across the country.”
An order of service will be available to download from King’s College from Friday for those wishing to follow it alongside the broadcast.
Their separate annual carol service, A Festival Of Nine Lessons And Carols, will be broadcast live on BBC Radio 4 at 3pm on Christmas Eve.
The college said it will go ahead without a congregation as a precautionary measure.