Kemboi, the 2004 champion, made the most of defending champion and compatriot Brimin Kipruto falling on the penultimate lap to sprint clear and win in eight minutes, 18.56 seconds.
Frenchman Mahiedine Mekhissi-Benabbad, a good friend of Kemboi, took silver and Kenya's Abel Mutai won bronze. Kipruto, who said he had been tripped, got up from his fall to finish fifth.
Flamboyant twice world champion Kemboi, who veered across the track with one arm raised in celebration in the final metres, was accused in June of stabbing a woman in Kenya, with the incident remaining unresolved coming into the Games.
Kemboi, a police officer, has rejected the accusation and Kenya's Olympic Committee (NOCK) cleared the 30-year-old to run in London, saying he was innocent until proven guilty by a court of law.
Kemboi announced his retirement from the track moments after victory to start a marathon career.
"I had planned to quit while at the top. I have two Olympic titles, two world titles and one Commonwealth title. That is enough. I will henceforth run marathon," he told reporters.
"We have been planning with my coach (Moses Kiptanui) about this and I feel this is the time to move on."
Kenya, who swept the medals in 2008, have won men's steeplechase gold at every Games since 1984.
Kipruto said he could not come back after being tripped with around 700 metres to go.
"I tried hard to recover but two athletes stepped on me while I was down," he lamented.
"I am devastated, but that is sport."
- Brimin Kipruto