Bekele, the reigning Olympic champion at 10,000m and 5,000m had hoped to use the three kilometre event in the Scottish capital to kick off a successful season heading into the Olympics.
However the 29-year-old Ethiopian was unable to make an impression over the Edinburgh course as world and Olympic 1,500m champion Kiprop romped to victory in 9min 20secs.
Kiprop bided his time over the opening stages before unleashing a blistering turn of speed to pull away from the field by a comfortable margin.
Former world 5,000m champion Eliud Kipchoge finished third after a battle for second won by British youngster Jonny Hay.
Kiprop was delighted with victory after going close last year.
"I expected a very tough competition from them," the 22-year-old Kenyan said of his big-name rivals. "I am excited having won here today after being second last year."
In the men's eight kilometre race, Spain's Ayad Lamdassem took the line honours in 25:44 with Bobby Mack of the USA second and Belgium's Atelaw Bekele in third.
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