Macdonald's wife Anna, who is Mr Guy's sister, held onto her father Bryan's arm and cried as the verdict was delivered.
Macdonald's parents, Kerry and Marlene Macdonald, sat on the opposite side of the court, behind the dock where their son stood.
The Crown alleged 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.
Macdonald, 32, denied murder.
During the trial, he admitted to burning down an old house on Scott and Kylee Guy's property, vandalising a new house being built there and stealing two deer from a neighbouring property.
Macdonald is yet to be sentenced on charges, including arson and criminal damage, to which he earlier pleaded guilty.
Justice Simon France remanded Macdonald in custody for a callover in Palmerston District Court on July 31, when a sentencing date would be set.
The Crown case was that 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 the identity of his killer remained a mystery.
The jury 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 trial.
Mr Guy's parents Bryan and Jo, older sister Nikki and younger sister Anna took the witness stand a number of times.
Reading a statement outside court this afternoon, Bryan Guy said the acquittal left the 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.''
Mr Guy said their lives had been "altered forever'' and the pain in their broken hearts was at times almost too much to bear.
But through the tragedy they had learned a lot about themselves, their values and what was important to them.
"We have learned how important a father is to his children. We now 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.''
He said the family was overwhelmed and touched by the love and caring of New Zealanders.
Mr Guy spoke of wanting to move on from the attention of the trial.
"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.''
Kerry and Marlene Macdonald gave no comment as they left court following the verdict.
Detective Inspector Sue Schwalger, who led the nine-month police investigation into Mr Guy's death, said police accepted the jury's decision.
"It has been a long and challenging two-year journey for everyone involved in both the investigation and the trial, especially the families, and I wish to acknowledge their strength and courage displayed throughout.''
She said police had conducted a professional and thorough investigation.
"Throughout this inquiry police have thoroughly investigated and assessed all information provided to them.
"Should anything new come to light it will be investigated with the same vigour, however we are not currently pursuing anyone else or any other lines of inquiry.''
Mrs Schwalger said the death would be referred to the coroner.
Rangitikei MP Ian McKelvie, who was Manawatu mayor at the time Scott Guy was murdered, said the verdict would be seen as inevitable.
He said the community would feel sympathy rather than anger towards the police and he believed the community would continue to support the Guy family.
THE SCOTT GUY TRIAL
- The trial in the High Court at Wellington spanned 21 days over more than four weeks
- The Crown called 77 witnesses and the defence called two witnesses
- Mr Guy's father and mother, Bryan and Jo Guy, and sisters Nikki Guy and Anna Macdonald - Ewen Macdonald's wife - gave evidence multiple times
- Dozens of exhibits were produced, including shoeprint impressions, dive boots, the Guy family shotgun, and a splitting axe Macdonald used to vandalise the Guys' new house
- The jury of 11 returned its verdict after 12 and a half hours of deliberations
FULL 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 now 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.''
