Macgowan will take up a midfield coaching role alongside Damien Hardwick, with the Hawks creating a two-man coaching team to look after the Hawks' talented midfield group.
The South Australian guided Sturt to a preliminary final this season, his second season at the helm.
Macgowan played 22 games for Central Districts, and played under Alastair Clarkson when he was in charge at the club, winning the 2001 premiership and finishing as runners up in 2002.
He said leaving the Sturt senior coaching position was "a really tough decision, because Sturt are heading in right direction as a team and as a club and it is a really special group of people there. But opportunities like this don’t come along too often.”
Macgowan said he was excited to be partnering Hardwick as midfield coach.
“Most clubs recognise the importance of the midfield in the modern game," he said.
"It is crucial to get the matchups and rotations right and continually develop each player in their particular role. I am excited to be working with such a committed midfield group as the current Hawks squad and helping develop some of the younger lads."
