The goals were the first scored by the Bosnian since he suffered a cruciate knee ligament injury in January.
Ibisevic needed only 44 seconds to hit the target when he volleyed in Chinedu Obasi's pass. He headed Hoffenheim's second in the fourth minute and struck again in the 21st with another header.
Raffael offered beleaguered Hertha hope when he pulled one back on the stroke of halftime.
But Nigerian Chinedu and Brazilian Carlos Eduardo, from a penalty, scored twice in a four-minute spell midway through the second half to complete the rout.
Hoffenheim climbed to third with 14 points from seven games while Hertha, who have lost six games, remained rooted to the bottom with three points.
Hertha appear to be suffering a hangover from last season when they were title contenders with only a few games remaining, only to finish outside the Champions League places following a late slump.
Hamburg SV, 1-0 winners over Bayern Munich on Saturday, lead with 17 points, ahead of Bayer Leverkusen on goal difference.
Promoted Freiburg beat Borussia Moenchengladbach 3-0 in Sunday's other game. Mohamadou Idrissou, Yacine Abdessadki and Julian Schuster were on target, all in the second half.
