Pictures posted on Twitter by the Royal Family and the Prime Minister shows the Queen on an old fashioned phone in her Berkshire royal residence and Boris Johnson in his Downing Street office holding a phone to his ear.
The weekly audience comes on the same day that Clarence House announced that the Prince of Wales has tested positive for coronavirus.
Buckingham Palace said the Queen, 93, who is staying at Windsor Castle with the Duke of Edinburgh, 98, remains in good health and is following all appropriate advice.
In the picture posted on Twitter, the monarch is in a room adorned with ornaments including a china corgi.
The royal family's tweet said: "The Queen held her weekly Audience with the Prime Minister today by telephone.
"Her Majesty - pictured this evening at Windsor Castle - has held a weekly Audience with her Prime Minister throughout her reign."
The Queen also had her weekly audience with Mr Johnson by phone last week.
On Wednesdays, the Queen holds an audience with the Prime Minister in the evening following PM's Questions in the House of Commons.
This can vary if either the Queen or the Prime Minister are away.
The day will either be changed or they speak on the telephone.
Members of the royal family have moved over to holding meetings by telephone as the coronavirus crisis deepens.
Charles, the Duke of Cambridge and the Earl of Wessex have all participated in telephone meetings or video conferences over the past couple of days.
The Queen is expected to make a public address to the nation at some point in the coming weeks and is likely to pay tribute to health workers treating the sick, sympathise with bereaved families and offer support to the nation living with the restrictions aimed at combating the virus.
A Buckingham Palace spokeswoman said: "Her majesty the Queen remains in good health.
"The Queen last saw the Prince of Wales briefly after the investiture on the morning of March 12 and is following all the appropriate advice with regard to her welfare."
On Wednesday evening, the royal family tweeted: "Thank you to organisations such as the @RoyalVolService who have been supporting and furthering this recruitment drive.
"Volunteers always have a huge role to play in society, but never more so than in difficult times - and for that we salute you."