The 30-year-old joined the Cherry and Whites in 2015 from Canterbury Crusaders and after an impressive first season he was rewarded with fresh terms in 2016.
Heinz was asked to captain the side on a number of occasions last season and he will take up the role on a permanent basis following Greig Laidlaw's move to Clermont Auvergne.
Director of Rugby David Humphreys believes Heinz has all the right qualities to be a good leader and believes he will excel in his new role.
Humphreys told Gloucester's official website: "Willi has developed into a true leader of this team, and we are delighted to confirm that he will be our captain for the new season.
"He is a player who leads from the front, and who truly has the respect of his team-mates, and all of the staff with the example he sets on and off the field of play.
"We speak about having a strong core of leaders in the squad, and Willi has been a key part of that during his time at the club, and he was an obvious candidate for the role, he will be continuing to lead the group to help drive this team forward."