The 45-year-old, who stepped up from assistant in December after Mark Burchill was sacked, has signed a one-year deal.
"Continuity is one of the main objectives of the board of directors," said a club statement.
"The club is also delighted that it will retain its full-time status."
Livingston had hinted at their intentions by announcing three new signings immediately after their play-off semi-final defeat by Stranraer.
Midfielder Jordan Sinclair, 19, arrived from Hibernian and central defenders Sean Crighton and Alan Lithgow joined from Airdrieonians.
Meanwhile, Ryan Currie agreed a new contract, but Bulgarian midfielder Spas Georgiev, who was loaned to Albion Rovers in February, was released.
Livingston have decided to remain a full-time club despite being relegated to Scottish League One and have handed head coach David Hopkin a new contract.