O'Brien, 58, was cleared of a further charge of threatening to kill Scott's gardener, Christopher Forster.
The jury of five women and seven men at Norwich Crown Court took nearly five hours to reach the 10-2 majority verdict following the eight-day trial.
The defence claimed O'Brien was guilty of manslaughter rather than murder, on the grounds of provocation.
But in sentencing him to life imprisonment, Mr Justice Blofeld said: "It is a terrible thing you did. For reasons difficult to fathom you totally lost your temper and in a moment of passion you picked up that gun and you shot Mr Scott." O'Brien had brought tragedy on everyone concerned, he added.
As the verdict was announced Scott's widow Julia, 38, who was flanked by members of her husband's family, let out a huge cheer.
Reading from a statement afterwards, Mrs Scott, who is left with three young children, said she was relieved the trial was over and that justice had been done. But she added: "Nothing will bring back my husband, senselessly killed in the prime of his life. He had so much to live for and look forward to both with his family and in his training career." She added: "He was the most wonderful husband and father and a very dear friend to all who knew him."
His brother Charles added that O'Brien had ended a "sparkling life".
Scott was shot in the back by a single barrel shotgun in a barn at Scott's Glebe Stud Farm in Cheveley, Newmarket, on 30 September last year.
During the trial the court heard how O'Brien had developed a "deep resentment" over Scott's working methods after the trainer took over the stud in 1992.
Matters came to a head three days before the murder when O'Brien apparently told a bloodstock agent that it was not convenient for buyers to view a horse. Scott took exception and in an argument, O'Brien told Scott he could "stuff his job".
The following day Scott sent O'Brien a letter asking for confirmation of his resignation.
According to Mr Forster, O'Brien apparently began planning a confrontation, and told him: "When he comes out I am going to have it out in the barn."
On the day of the murder, Scott visited the barn to remove O'Brien's belongings. After everything had been cleared out, O'Brien insisted Scott had a look in the barn "to make sure everything was all right".
The court heard that moments later Mr Forster, who was outside, saw O'Brien standing over Scott, aiming the shotgun at him and firing, saying: "This is for you, you bastard."
After threatening to shoot Mr Forster, O'Brien was interrupted by the appearance of his wife, Helen, and Mr Forster ran off to warn Mrs Scott.
O'Brien disappeared, apparently with the intention of killing himself, but was found by police the following morning.
In a police interview O'Brien said: "I don't know what happened, I just went. I have had so much with that man since 1992 it's unbelievable. He has driven us around the bend with his language, his abuse, his shouting."
He said he had not intended to shoot Scott: "I just took the gun up and fired it at him."Reuse content