The prosecution had alleged Mr Barker was tied to a tree with honey smeared on his genitals to attract ants.
He may have had fingers cut off as he was tortured for information, the court also heard.
According to local newspaper The Gympie Times, prosecutor Glen Cash claimed the older Armitage told a witness: "We smashed his kneecaps in, broke his fingers.... smashed his face in. You wouldn't even recognise him."
The report said both men cried out after the verdict was handed down, with Stephen Armitage saying: "Injustice, your Honour. Didn't do it".
The Times said his son added: "I didn't do it".
Shaun Barker was reported missing by his family on January 14, 2014.
The 33-year-old's charred remains were found in the Tooloora State Forest near Gympie on April 10 that year.
The two are due to be sentenced later this year alongside William Francis Dean, who was also found guilty of murder in March 2017.