Stevens, 61, twice came to the rescue of VfB Stuttgart in the past two seasons, taking over midway and late in the campaigns and avoiding going down.
"It was not an easy decision," sports director Alexander Rosen said in a statement on Monday. "We showed calm and patience with Markus' work."
Hoffenheim lost 1-0 to Hamburg SV on Friday and have managed just one win in 10 league matches this season. They are second from bottom on six points.
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Gisdol took over in April 2013 and also helped the team, backed by billionaire Dietmar Hopp, stay up last season.
Veteran Stevens has twice coached Schalke 04, including their UEFA Cup-winning season in 1997, and also worked at Hamburg SV, Hertha Berlin and Cologne.
(Reporting by Karolos Grohmann; Editing by Tony Jimenez)
