She was left stranded in Abu Dhabi after the 23-year-old Airbus A340-300 had repeated wing flap problems.
"This is beyond annoying," the minister wrote on X, formerly known as Twitter.
Germany may enjoy a reputation for efficiency, but its government planes are notoriously unreliable.
In 2018 the same Airbus plane had a technical fault which forced the then Chancellor Angela Merkel to miss the opening of a G20 summit in Argentina.
Earlier that year, Olaf Scholz - Germany's finance minister at the time and now chancellor - was stranded in Indonesia after rodents chewed through cables on that plane.
Ms Baerbock was en route to the Indo-Pacific on Sunday when the wing flaps on her plane malfunctioned, forcing the pilots to make an emergency landing in the United Arab Emirates.
After repairs and a successful test flight, the aircraft took off again on Tuesday - only for the same problem to arise.
In the end, the minister was forced to cancel her planned week-long trip. Her team could not be booked onto commercial flights within the time schedule.
"We have tried everything: unfortunately it is logistically impossible to continue my Indo-Pacific journey without the defective plane," Ms Baerbock wrote on X.
The plane had to dump fuel in order to land back in Abu Dhabi safely.
Owing to the mishap, Germany's Luftwaffe Air Force announced that it would retire the plane early. The government's other A340-300 will also be replaced.
"We will take the two #A340 out of service as soon as possible, ie in the coming weeks," it said in a post on X.
Instead, top government officials will soon be using recently bought A350 planes.
"With the A350s, the Air Force has robust and modern aircraft at its disposal for long-haul operations," the Luftwaffe said.
In May Mexico also finally resolved a government plane problem: for more than four years it had failed to sell a luxury presidential jet, but in the end the Tajik government bought it.