The 61-year-old Dutchman took charge of first-team duties on 25 November 2014 after Armin Veh stepped down with the club at the bottom of the table.
The Swabians eventually secured their Bundesliga status for another season on Matchday 34 with a 2-1 win away to fellow strugglers SC Paderborn, who were subsequently relegated. Stevens also saved Stuttgart from the drop last term, coming in with ten games to spare and helping them finish in 15th.
"Huub Stevens was named coach of the century at another club, but with us he's been the saviour of the century," said Stuttgart sporting director Robin Dutt, who confirmed Stevens' departure on Sunday morning in an interview with German television station Sport1, but said no successor had yet been lined up. "Huub has done exceptional work here. It wasn't just that he saved us from relegation twice, but working together with him was super. For this reason alone we owe him a huge debt of gratitude."