Teenager Kipruto, who won gold medals at the 2011 world youth championships in Lille, France, and the world junior championships in Barcelona last year, reaffirmed his hunger for bigger titles with his third victory over Kemboi this season.
Kipruto bagged automatic qualification to the world championships in Moscow after winning the much-anticipated race in 8:13:50.
Abel Mutai was second in 8:14:00 and Brimin Kipruto, who won the Olympic title in Beijing in 2008, was third in 8:14.90.
Kemboi finished in sixth position, but was still selected to defend the world title he won in Daegu.
Brimin Kipruto was excluded from the team for Moscow.
The top two finishers gained automatic selection for the Aug. 10-18 championships, while the third spot was awarded by the selectors.
Olympic champion and world 800m record holder David Rudisha was left out of the team altogether because he failed to take part in the trials as he is undergoing treatment for a knee injury in Germany.
Rudisha, who set a world record of 1:40.91 in winning the Olympic title last year in London, picked up the knee injury running in Central Park in New York.
Conseslus Kipruto has won in all the Diamond League meetings this year, beating Kemboi in Eugene and Oslo, although Kemobi ran the world-leading time of 7:59.03 in Paris last weekend.
World 1,500m champion Asbel Kiprop, who won gold in the 2008 Olympics in Beijing, was beaten into second position by world silver medallist Silas Kiplagat, who won in 3:33.70.
Vivian Cheruiyot, who won the 5,000m and 10,000m in Daegu and is expecting a baby, missed the trials as did Sally Kipyego, the 10,000m world and Olympic silver medallist.
- Sports & Recreation
- Brimin Kipruto