The 37-year-old player/coach had been in interim charge of the Ladbrokes League 1 team and guided them to a memorable Scottish Cup win over Falkirk at Ochilview on Saturday to set up a fourth-round tie with Aberdeen at Pittodrie.
Chairman Iain McMenemy told the club website: “We had a number of applicants for the position and held a thorough process of evaluation and multi-stage interviews.
“Colin was strong throughout - he really stepped up and set out a clear vision of where he wanted to take the team and his positivity was clear for us all to see.”