Mr Guy's wife Kylee Guy cried out "he killed my husband'' in tears and stormed from the courtroom. Mr Macdonald was tearful as the verdict was given.
The Crown alleged Mr Macdonald shot and killed Mr Guy, 31, at the end of the driveway of his Feilding home in the pre-dawn darkness of July 8, 2010.
Mr Macdonald, 32, denied murder.
The jury of seven men and four women delivered their verdict in the High Court at Wellington after deliberating for 12 and a half hours.
Their deliberations began about 11.30am yesterday after Justice Simon France summed up the four-week case. The jury retired about 5pm yesterday and resumed deliberations at 9am today.
The Crown case was that Mr Macdonald killed his brother-in-law after tensions over the future of the family farm they co-managed.
His defence team said the problems on the farm had all been resolved and his killer remains a mystery.
The jury have heard more than three weeks of evidence and submissions from prosecution and defence lawyers, who gave their closing addresses late last week.
The relationship between the two men and the workings of the family farm were constant threads throughout the four week trial.
Mr Guy's parents Bryan and Jo Guy, older sister Nikki Guy and younger sister Anna Macdonald, the accused's wife, took to the witness stand multiple times.
It was only last week, after they had finished giving evidence and the closing addresses got underway, that they were able to sit together in the courtroom's packed public gallery.
In his closing address last week, Crown prosecutor Ben Vanderkolk said Mr Macdonald had deep-seated anger and resentment towards his brother-in-law and, despite efforts to resolve the issues, those feelings never went away.
He said Mr Macdonald set about "failed, intensifying efforts'' to intimidate Mr Guy and his wife Kylee off the farm by putting "poisonous letters'' in their mailbox, burning down an old farmhouse on their property and vandalising a new house being built there.
Mr Guy's murder was "intensely personal'' and only Mr Macdonald had the knowledge and ability to do it.
In his closing address, defence lawyer Greg King said the reality was Mr Macdonald and Mr Guy had been getting on better than they had in years, and were positive about the future.
Mr Macdonald admitted to and regretted the arson and vandalism attacks, and had been making steps to move on from his "appalling'' behaviour.
He did not admit the arson and wilful damage until later because if he had, he would have "lost everything'' - including his family.
Mr Macdonald later told the truth to police and denied penning the letters or killing Mr Guy.
Mr King said evidence on the timing of Mr Guy's death, the number of shots fired, a mystery car seen about the time of the murder, and other aspects of the police investigation had raised enough reasonable doubt.
Guy family statement, read by Bryan Guy
"We have been overwhelmed and touched by the love and caring of New Zealanders.
"The support and prayers of friends and strangers alike in our local community and throughout the country have given us strength and courage.
We are forever grateful to everyone for their kindness to us and our family.
"The acquittal today leaves our family with mixed emotions. While we are relieved the trial is over we are obviously left wondering who is responsible for the death of our son.
"This verdict today will not bring Scott back. This verdict will not restore a father to his children. It will not restore a husband to his wife. It will not restore a son and brother to his family.
"Our lives have been altered forever. The pain our our broken hearts is at times almost too much to bear. However, through this tragedy we have learned a lot, mostly about ourselves, what we stand for, what our values are, what is important to us.
"We have learned how important a father is to his children. We know that a father can never be replaced, but with strong family and community values and support, there is hope for the future.
"We are thankful for how Scott touched our lives and we are richer for him being part of it.
"We must focus on what we have, not what we have lost.
"We are determined to love and support our children and grandchildren in their future. Our family is grateful for the generosity of so many people.
"It reminds us that the world is full of good people who really do care. Thank you all for that reminder, and thank you all for your love and support.
"During these past weeks and months our lives have been an open book to the nation. We now wish to close this chapter and take time to pause and reflect away from the publicity and begin to rebuild our lives.''
