The trio were found guilty in 2021 over a rigged coal exploration licence tender following a lengthy investigation by the NSW Independent Commission Against Corruption.
On Friday, the NSW Court of Criminal Appeal dismissed a bid to have their convictions overturned.
Eddie Obeid became a symbol of political corruption in NSW and spurred a crackdown on unethical behaviour in the state's upper echelons.
Macdonald conspired with the Obeids over a coal exploration licence covering their property.
In October 2021, Justice Elizabeth Fullerton jailed the now close to 80-year-old for at least three years and 10 months, his son for at least three years and the now 74-year-old Macdonald for at least five years and three months.
She found all three guilty of conspiring for the then-state resources minister Macdonald to engage in misconduct between 2007 and 2009 following a long and complex judge-alone trial.
Because of the unusual nature of the case, Justice Fullerton's initial judgment spanned 670 pages and included more than 2000 footnotes.
Macdonald was found to have provided confidential information to the Obeids about a coal exploration licence covering a property the family owned in the Bylong Valley, which ultimately delivered a $30 million windfall to their family.
Lawyers for the Obeids challenged their convictions on a range of grounds, including Justice Fullerton's reasoning, while Macdonald's representatives argued it couldn't be proven he knowingly entered into an agreement to engage in corruption.
It was also argued that on May 9, 2008, when Macdonald first sought information regarding the volume of coal reserves on and around the Obeids' Cherrydale Park property, he did not know they were the owners.
But the appeal judges concluded the prosecution had proven beyond reasonable doubt a conspiracy existed and was carried out by the trio.
Macdonald failed to get his jail sentence reduced in a separate appeal.
On Friday, Macdonald failed in a separate appeal to have his sentence shortened.
His lawyers argued, among other grounds, that the five-year minimum sentence was manifestly excessive and the judge's conclusion that the objective seriousness of the conspiracy was "of the highest order" was not correct.
Chief Justice Andrew Bell was one of three judges to uphold the sentence, calling it appropriate and in line with the gravity of the offence.
"Actions utterly corrosive of public trust by a minister of the Crown do unquantifiable damage to our democracy," he said.
