The popular hosting duo, who usually front the programme from Mondays to Wednesdays each week before handing over to Naga Munchetty and Charlie Stayt, were replaced by relief presenters Ben Thompson and Tina Daheley.
Although Sally's absence from the show hasn't been explained, it's likely that she's taking a planned break from the show for the summer, or she's simply booked the day off.
As for Jon, the journalist explained in a statement shared on Sunday night that he would be taking "long-planned annual leave" to spend time with his family but will return to the sofa in two weeks' time.
"Enjoying some extra sleep and long-planned annual leave with the family, so no need to set my alarm clock tomorrow morning," the 53-year-old wrote on social media. "Back on the red sofa with my BBC Breakfast family in Salford in two weeks' time."
The show's viewers took to the comments section to wish Jon a relaxing break, with one person writing: "Enjoy your holiday and especially the extra sleep. Look forward to seeing you on the red sofa in two weeks' time."
Other fans said it was a "shame" that Jon had to explain his absence from the current affairs programme, making reference to the suspension of an unnamed BBC presenter who has been accused of paying a teenager thousands of pounds for sexually explicit photos.
One follower commented: "Shame you've had to justify your time off. Enjoy, you will be missed!"
While BBC Breakfast viewers are no doubt missing Jon and Sally on their screens, they are in good hands with Ben and Tina.
For those unfamiliar with the presenters, Ben is a regular stand-in on the show and is also a newsreader for BBC News.
Meanwhile, Tina reads the news on The Radio 2 Breakfast Show with Zoe Ball and also regularly appears on BBC News at Six and at Ten.
Sally and Jon aren't the only two stars missing from their regular spots on the show as business presenter Nina Warhurst is also away.
The 42-year-old signed off on maternity leave towards the end of June and just weeks later welcomed her third child, a little girl, with her husband Ted.
Announcing the exciting news on BBC Breakfast, Jon and Sally informed viewers that the family are "doing well" and that the "healthy" newborn's name is a "work in progress".
Nina, who is already a doting mum to two sons, Digby and Michael, later shared an update with her social media followers and said that the family are "all well and loved up". She also thanked the staff at St. Mary's Hospital in Manchester, which is where she delivered her baby.