The 46-year-old Stoeger, who already led the team to an Austrian league victory in 2006, signed a two-year contract with the club, Austria Vienna announced on its official website.
"It's good to be back," said Stoeger. "I spent much of my career here and had many great successes. We last won the championship in 2006 and we want to continue to work in that direction in the future."
As a player, Stoeger spent eight seasons with Austria Vienna, winning three championships.
He also led the team to two Austrian Cup wins in 2005 and '06, as coach alongside Frenkie Schinkels.
Stoeger replaces former Sturm Graz star and Austrian international Ivica Vastic, 42, who took over in December but whose contract expires in May.