The presenter was absent from the start of her live broadcast at 7am, and had to leave prior to her show finishing, with travel reporter Richie Anderson standing in.
Zoe had arrived 30 minutes late for her show after her car suffered a flat tyre.
“Bit of a drama on a Monday morning,” she said, as she finally came on air. “Nothing like that to start you off on your week. Richie, what a star.”
However, Zoe had to step off the microphone again after becoming unwell later in the show.
Richie continued to present until 8.30am, at which time Ken Bruce came on air an hour before his scheduled slot.
Zoe later assured fans she was doing OK, revealing the drama earlier in the morning had taken it out of her.
She tweeted: “Apologies for this morning gang, tyre went on the way in to work. I was so keen not miss the show, dashed in and hadn’t quite realised the effect it’d had on me. i’m ok. thanks for the lovely messages.
“Big thanks to Richie and Ken for stepping in. will be back tomorrow xx.”
The Zoe Ball Breakfast Show airs weekdays from 7am on BBC Radio 2.