The journalist usually appears on the programme from Monday to Wednesday every week but was replaced by relief presenter Ben Thompson, who regularly steps in for the main hosts when they are away.
Jon became a main presenter last year following the departure of Dan Walker, who left to host 5 News.
The 53-year-old isn't the only star absent from the show as weather presenter Carol Kirkwood was also nowhere to be seen, with Matt Taylor standing in with the latest weather updates.
Carol has been away from the show since last week, with both Matt and Sarah Keith-Lucas taking turns to cover for the Scottish star.
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While Carol has yet to address her absence, it's likely that she's simply taking a well-deserved break and is on annual leave.
During her time off from the programme, Carol is no doubt enjoying spending some quality time with her fiancé Steve Randall.
Carol announced her engagement to the former police officer during a live weather report from the Chelsea Flower Show in May last year, which you can watch in the video below.
Speaking about the early days of her romance with Steve, Carol explained that the couple's relationship naturally evolved from friendship. "We were friends before we became romantically involved so we knew each other quite well before we started dating," she told Closer magazine. "That was nice because it just kind of happened.
"Neither of us were looking for romance and there it was, it just evolves. It's so lovely. Who'd have thought that at this ripe old age, I'd be getting married again? I certainly didn't."
Both Carol and Steve will be able to enjoy a lie-in while the presenter takes a break from BBC Breakfast as the Scottish star previously revealed that her partner wakes her up with a cup of tea when her alarm goes off at 2.45am for work.
"Even though I say to him every time, 'Don't get up, you go back to sleep,' he always insists on getting me my tea," she told The Mirror.
As for when they'll walk down the aisle, Carol explained that the couple haven't put a date in the diary just yet. "I do want to get married again. We're very happy and we're loved up, and we're delighted to be together, but we haven't got a wedding date yet," she said.
Sharing her hopes for their big day, she continued: "I think we'll have an intimate wedding. We don't want to just squeeze it in, we want it to be a celebration."