Appearing alongside his Take That bandmates, the singer started to respond to a question from presenter Richard Osman before saying he felt unwell and leaving Howard Donald and Mark Owen on the BBC sofa.
Barlow said: "Can I leave you guys to it? I don't feel very well, excuse me," and walked off set, leaving viewers bemused.
However, the singer managed to return several minutes later for a performance of the band's latest single, We Are Giants.
The incident left Osman and fellow presenter Angela Scanlon confused as they attempted to continue with the interview.
Making light of Barlow's departure, Owen said it was a "bit weird now" before also jokingly leaving the set.
In a post on Twitter minutes after the show ended, Barlow said he was "absolutely fine".
He wrote: "Thank you all for the messages. I'm absolutely fine. We had a very hot dressing room and I thought I was going to faint on live TV."
The trio were on the BBC show to promote their upcoming tour and latest album, Wonderland.