They've been searching for alternative approaches to pollination, because of the decline in the number of bees worldwide.
When fired from a bubble gun, the delicate soapy spheres achieved a success rate of 95%.
The researchers are now testing drones that fire bubbles for pollination.
Dr Eijiro Miyako, from the Japan Advanced Institute of Science and Technology, had previously tested the ability of a drone to deliver pollen - but even though the drone was just two centimetres long, it kept damaging the flowers in the process.
One day, while watching his young son play in a local park, Dr Miyako had a moment of inspiration.
"I was playing soap bubbles with my son at a park close to my home, when a soap bubble accidently hit my son's face," he told BBC News.
"There was no damage because soap bubbles are soft, light, and flexible."
"But I got an inspiration because I thought the bubbles won't damage the flowers and would be an ideal material for pollination."
Dr Miyako commandeered the bubble solution, causing his son to start crying and necessitating the purchase of more bubbles.
In the lab, he was able to confirm, via optical microscopy, that soap bubbles could carry pollen.
Realising that most conventional soap would be too toxic for flowers, Dr Miyako developed what he terms "chemically functionalised" soap bubbles that could each carry up to 2,000 pollen grains.
Loading up their bubble guns, Dr Miyako and his colleagues tested the technique at a pear orchard.
In the absence of bees, some pollination work is now done by hand using a feather brush.
After shooting the bubbles onto the trees, young fruits started to form some 16 days later, at a volume equal to the hand pollination.