There were gasps of surprise as High Court Justice Muga Apondi gave his ruling after reading out a 320-page verdict on the case, although the defendant himself remained impassive.
"I find as a fact that it was the accused who had shot the deceased resulting in his death," the judge said.
"In view of the above analysis I hereby find which I do, that the accused did not have any malice aforethought to kill the deceased."
The Eton-educated 40-year-old, who has spent the last three years in jail, is due to be sentenced next week. He faces a maximum term of life imprisonment.
"I'm amazed - dumbstruck actually," said Cholmondeley's defence lawyer. "We will appeal. There is no doubt about that."
The incident took place in a remote corner of Cholmondeley's sprawling family farm in the Rift Valley region, acquired by his great-grandfather, the third Baron Delamere.
Cholmondeley told police at the time that Mr Njoya was with three companions and a pack of dogs, and he suspected them of hunting a gazelle.
He said he had shot at the dogs, killing two of them. Mr Njoya was hit by a bullet and died on the way to hospital.
Cholmondeley's defence had argued that the fatal shot may have been fired from a weapon carried by his friend, but this was rejected as an "afterthought" by the judge.
The judge's verdict is contrary to the non-binding not guilty verdict found by a panel of lay assessors - who do a similar job to juries in Kenya - in March.
The outcome will surprise some who followed the case closely, our correspondent says.
But it will please those Kenyans who believe Thomas Cholmondeley should have been prosecuted over the shooting of Maasai ranger Samson Ole Sisina in 2005.
Cholmondeley, a divorced father of two, had admitted the earlier shooting, but said he acted in self-defence mistaking the warden for an armed robber.
The latest trial has stirred up lingering animosity against some in the white farming community, who are accused of living on large areas of land, illegally grabbed early last century, our correspondent says.
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