The 45-year-old has left Stirling Albion to replace James Grady at the club where he spent a brief spell during a 20-year playing career.
Grady, who took over on a temporary basis when David Irons was dismissed last September, was not offered a new contract after the Greenock club finished eighth in the Irn-Bru First Division.
Moore - who Morton failed to land after sacking Irons - will face Stirling next season after leading them to the Second Division title in his eighth year at the helm.
He said: "I have served a long apprenticeship at Stirling and I suppose I will no longer be referred to as Scotland's longest-serving manager after this move.
"I am delighted to be given the chance to be here; it could have happened a few months ago but it has happened now so I am delighted."