He was 78 and had been battling lung disease.
He is best known for being the father of Dr Who actor David Tennant and presenting STV's religious magazine programme 'That's the Spirit'.
Dr McDonald was an outspoken advocate of assisted dying since revealing he was fighting the degenerative lung disease pulmonary fibrosis.
"Sandy didn't just preach. He put his whole self into it— his arms, his voice, his whole body went into his sermons," said Very Rev Dr Lorna Hood, Dr McDonald's lifelong friend and minister since his retirement.
"People loved it when he preached."
"He was a great pastor and he held parish ministry at the heart of the Church."
He was Moderator from 1997-98 and was being cared for at the Erskine Care Home for ex-servicemen in Bishopton.
He was called up to do national service, enlisting in the Royal Air Force where his duties included operating ground radar for the 617 Dambusters.
Very Revd John Chalmers, the Church's Principal Clerk, has known Dr McDonald since the 1970s and worked with him during the 20 years he served as Secretary of the Ministries Council.
"Working with Sandy Macdonald was one of the great pleasures of my career in ministry," Mr Chalmers said.
"Sandy would be best described as an enthusiast and the Church of Scotland benefited from that enthusiasm from the day and hour that he committed his life to its ministry."
Dr McDonald was also known for presenting STV's religious magazine programme 'That's the Spirit' during the 1980s, and was a guest on other religious shows.