The music legend, worth around £600 million, was flying from Heathrow with Air Portugal earlier this week when the crew told passengers that the plane had to refuel in Porto instead.
The American, 59, looked tired as she wore a long, black and white multi-checked coat, a monochrome striped scarf and hid her make-up free face under a grey fedora hat, reports Daily Mail.
She had been hiding completely unrecognised in the cheap seats - which cost from just £42 instead of £180 for business class tickets - until the flight landed in Porto and her agent whisked her through business class to the front of the plane.
An onlooker said: 'We'd been on the ground for about 20 minutes when I saw her assistant speaking with crew members at the front of the plane. Then I noticed all this Louis Vuitton luggage being carried past me down the aisle too. And Madonna literally walked by me. I couldn't believe it. She had no make-up on but I Googled her and I discovered that she's recently bought a place in Lisbon, so her being on the flight suddenly made sense.'
'I thought to myself 'Madonna is on my flight!'
'She looked tired as she sat and waited at the front of the plane for about half an hour. I could barely see her face, she was constantly turning away or hiding her face in her scarf. She didn't say or do anything while her agent was on her phone. Madonna was just sitting and waiting. Then she got off the plane and I saw her get on to an airport bus. I'd heard her agent saying that her car was waiting out front - they must have meant outside the airport.'
The assistant appeared to have told the crew she was Madonna but they remained professional and didn't react. No one else appeared to recognise the Holiday superstar in their midst.
The lunchtime flight sat on the Porto runway for about an hour before flying on to Lisbon.
The source continued: 'Then a lady asked why two women had left the flight at Porto. A female crew member whispered to her that it was Madonna. She was gobsmacked!'
The rest of the passengers eventually arrived in Lisbon three hours late yesterday evening.
When MailOnline spoke to Madonna's publicist Barbara Charone about this story, she refused to comment.
A spokesman for TAP said heavy rain in Lisbon meant there was bad air traffic over Lisbon.
The pilot was told that they would be in a holding queue for half an hour when they got there so they decided to touch down, he said.
The spokesman added that while TAP always carried sufficient fuel they decided that the better course of action was for the plane to land in Porto.
'TAP confirms Flight TP359 from November the 28, from Heathrow to Lisbon, diverted to Porto (distance between the 2 cities around 300 km) due to bad weather in Lisbon.'