The U2 frontman was on board a Learjet 60 D-CGEO with four friends flying from Dublin, Ireland to Berlin, Germany when the tailgate of the plane became detached at 8,000ft, but the party - which did not include the rest of the group - didn't realise what had happened until they landed.
A source told the Irish Daily Mail newspaper: "He was extremely lucky, the plane could have gone down. About an hour into the journey they heard a big thud coming from the rear of the plane.
"They were startled for a bit but they continued on and made the descent into Berlin airport. When they landed they were horrified to learn that the compartment at the rear of the plane had completely detached.
"They were at an altitude where anything could have happened and they are all feeling very lucky to be alive."
As a result of the accident, Bono and his friends' luggage fell out of the plane.
The source added: "The entire door, along with Bono and his companions' luggage, had fallen out mid-air. They don't know if the door and the contents landed over water or land but they were extremely lucky."
Aviation authorities in Germany have launched an official investigation into the incident, and police and officials from the German Federal Bureau of Aircraft Accidents Investigations Office were spotted scouring fields near the airport this morning (13.11.14) looking for the luggage and other debris.
Airport spokesman Ralf Kunkel said: "The jet landed safely and, according to our knowledge, there was no danger of a crash."
Bono - who had flown out early to meet with Germany's development minister Gerd Mueller - and the rest of U2 appeared later on Wednesday night performing at the Bambi movie awards in Berlin.