The 48-year-old sat alongside co-host Dan Walker for the first part of the morning show, but when the camera cut back to them after the news, travel and weather, she was no where to be seen.
Explaining what had happened to viewers at home, Dan said: "Good morning everybody, this is BBC Breakfast with Sally Nugent now and Dan Walker.
"Louise isn't feeling particularly well, so you're going to have to double shift it if that's alright?" he added to Sally.
"Yes that's fine," she replied. "Sorry to confuse you everybody, I just stepped in at the last moment, so bear with me."
Louise Minchin disappeared halfway through presenting BBC Breakfast today
Nice cuppa and some paracetamol will sort her out. Hope she feels better soon
Dan later tweeted: "I'm sure @louiseminchin will be ok. Nice cuppa and some paracetamol will sort her out. Hope she feels better soon."
Understandably, viewers were left feeling worried for Louise, who appeared fine earlier on in the show.
One Twitter user posted: "Louise are you ok? I was watching Breakfast and one minute you were there, then I had to leave room and when I came back it was a different presenter."
Then another added: "Hope you feel better soon @louiseminchin. Sterling work from @sallynugent.. bosses PLEASE take note! Love the banter with Dan."
Following the travel and weather segments Dan Walker returned with Sally Nugent by his side
I'm sure @louiseminchin will be ok. Nice cuppa and some paracetamol will sort her out. Hope she feels better soon.
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— Dan Walker (@mrdanwalker) February 1, 2017
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BBC Breakfast thought Dan's bird print shirt might have made Louise unwell
Other viewers blamed Louise's sudden illness on 39-year-old Dan's choice of attire.
"Get well soon Louise, think it's a delayed migraine from that shirt yesterday," on person commented, while another wrote: "@BBCBreakfast @louiseminchin @sallynugent @mrdanwalker could have been dans tie turned your tummy."
The presenter was mocked online yesterday after wearing a white shirt which was adorned with images of ducks, swans and other birds.
The £145 garment certainly got people talking with the majority mocking his smart shirt
However, Dan responded by tweeting: No, it wasn't dark when I got dressed. No, I haven't nicked Lou's blouse, or cut-up a curtain. No, I didn't lose a bet #ShirtGate #Birds."
BBC Breakfast continues weekdays at 6am on BBC One.