Roberto Firmino's early strike and an Andreas Lambertz own goal put the hosts on their way to victory before Kevin Volland sealed all three points for only the sixth time this season, allowing them to creep up on Augsburg in 16th place.
Hoffenheim looked transformed from their fourth change of coach this season and only what appears to be a serious hand injury to goalkeeper Heurelho Gomes cast a shadow on a successful night at the Rhein-Neckar Arena.
Hoffenheim are now just a point below Augsburg, who are in action against Borussia Dortmund on Saturday, in the relegation play-off berth with Fortuna just five points further ahead with six games of the season remaining.
Gisdol kept the changes to a minimum, but what he had altered was his side's frame of mind.
They were aggressive from the whistle, crushing Fortuna inside their own half with the returning Sejad Salihovic instrumental at the heart of midfield.
Just 11 minutes were on the clock when Sven Schipplock set up Firmino to drill a shot high into the roof of the net.
Fortuna appeared stunned by the force of the home team's attacks and they were forced into damage limitation before finally gaining the courage to attack themselves.
Robbie Kruse, who passed a late fitness test to appear for Fortuna, was their most creative outlet on the right wing and his cross on the stroke of half time was headed wide by Axel Bellinghausen.
It was an important sign of life from the visitors, who started the second half with much more confidence, although Lambertz was a touch overzealous as he stretched out a foot and caught Gomes who, after several minutes of treatment, had to leave the field.
Koen Casteels came on, yet he was never really put to the test as Hoffenheim launched a second wave of attacks, grabbing a second goal with 15 minutes remaining.
Salihovic's corner was diverted into his own goal by the head of Lambertz as he tried to make a clearance.
Volland wrapped up victory in the last minute of stoppage time, keeping his cool to beat Fabian Giefer after being put through on goal by an inspirational Salihovic.