Naismith has been named as technical director with Frankie McAvoy as head coach, in order to comply with UEFA regulations until the former Scotland international earns his Pro Licence coaching qualification. Gordon Forrest will remain as first-team coach.
The former Kilmarnock, Rangers, Everton, Norwich and Hearts player took charge of the final seven games of the season and kept the Jambos in fourth place in the cinch Premiership.
Chief executive Andrew McKinlay said: “We are thrilled to confirm Steven, Frankie and Gordon as our coaching team.
“We received a number of excellent applications, and, after a robust recruitment process, we believe the three were the best candidates to lead us into next season while sharing our vision for the club’s future.
“Steven is an outstanding young coach with a strong track record of improving players whilst also displaying a commitment to blooding young talent through the ranks.”