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.

Swansea University analysed data from nearly 360,000 children aged between six and 18 between 2003 and 2013.
It followed a health warning in 2003 that children should not be given most antidepressants.
The unpublished research triggered a Welsh government circular saying other methods should be tried first.
The 30% rise came despite a significant fall in 2003-4 following health warnings about the risk of suicide in young people.
The report, which has not been published, also showed the drug citalopram was routinely prescribed despite not being licensed for use in children.
The Welsh government wrote to health professionals that only fluoxetine (Prozac) has been shown to be effective in young people.
A Welsh government spokesman said it expected GPs to use their clinical judgment in deciding treatment, and to use NICE guidelines which recommend psychosocial interventions should be considered as an alternative to antidepressants.
The report said the figures could reflect better access to treatment, and a positive shift towards helping people address mental health issues at a younger age.
But it added: "On the other hand this may represent an increasing tendency to prescribe medication where other treatment options such as psychological therapies are limited or not available at a primary care level.
"This may be a particular issue in more deprived areas where incidence is nearly double that in more affluent areas."
It comes as research has shown a 54% increase in the number of children and young people prescribed antidepressants in the UK between 2005 and 2012.
George Watkins, 20, from Cardiff, experienced side-effects after being prescribed antidepressants as a teenager.
"I would open my eyes in the morning, I still get nightmares about this, about waking up every morning staring at the ceiling and wondering if this was the day when I would feel clear-headed.
"It was a very rushed appointment, it was five minutes, 'describe what you're feeling'.
"I was still on the medication that I was prescribed when I was 14 or 15 last November, when I had just turned 20," he said.
Children's Commissioner for Wales Sally Holland told BBC Wales the long-term effects of anti-depressant drugs in children were not really known.
"NICE guidelines are very clear: children and young people must have medication as a last resort," she said.
"There should be a month of careful watchfulness and then they should be offered psychological therapies and they should only be offered medication along side psychological therapies if the therapy doesn't work.
"It seems sad to me that George hasn't had that."
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.
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There has been a 30% increase in the number of children in Wales prescribed antidepressants over 10 years, figures obtained by the BBC have shown.