The changes are effective from February 1, 2023 upon the expiration of the contract of current MD Sport Jörg Schmadtke.
Schäfer (pictured), 38, has signed a new three year contract and will work closely with Schindzielorz, who left his role as Director of Sport at VfL Bochum this month.
Schindzielorz has signed a contract until June 2025.
The pair played together for Wolfsburg, winning the Bundesliga title in 2009.
Frank Witter, Chairman of the Supervisory Board, said: "Marcel Schäfer has had close ties to VfL Wolfsburg for many years. Even as a player on the pitch, he embodied the virtues of VfL, with which he has also successfully mastered his duties as sports director since 2018. It has been proven that Marcel Schäfer not only has a very high level of sporting expertise, but also identifies one hundred percent with the club and the region."
Schäfer added: "I am very happy about the trust that is placed in me and my work. Following in Jörg Schmadtke's footsteps will be a great challenge, which I will tackle with great joy and enthusiasm. I've been working closely with Jörg for over four years and I'm very grateful that he gave me the opportunity to learn, to work independently and to develop myself further every day."
Schäfer became Sporting Director ahead of the 2018-19 season, and has overseen a recruitment policy focused on young talent, as he told TransferRoom in an exclusive interview earlier this year.
Schmadtke has been MD Sport at Wolfsburg since June 2018, having held the same role at first Hannover 96 and then 1. FC Köln.