His dismissal came after Mainz's defensive midfielder Jean-Philippe Gbamin was also sent for an early shower.
Both teams finished with ten men for the final quarter of an hour as Ibisevic was sent off for receiving his second yellow card.
His dismissal came after Mainz's defensive midfielder Jean-Philippe Gbamin was also sent for an early shower, also for a second booking.
"We stayed calm despite conceding the early goal, got ourselves level and then created the winner, so we deserved the win," said Hertha coach Pal Dardai.
Aaron Seydel had given Mainz the lead after 25 minutes at Berlin's Olympic Stadium, but Hertha responded when Salomon Kalou spotted Ibisevic unmarked and the Bosnia forward fired home Berlin's equaliser on 36 minutes.
Gbamin was sent off on 62 minutes and his dismissal changed the course of the game.
Kalou and Ibisevic combined again for Hertha's second.
Ivory Coast international Kalou headed back across goal on 67 minutes for his forward partner Ibisevic to fire home before he was sent off seven minutes later.
Hertha climb to third behind leaders RB Leipzig and second-placed Bayern Munich.
Earlier, Schalke 04 continued their rise as striker Eric Choupo-Moting atoned for a penalty miss by netting in their 3-1 comeback win against Darmstadt.
Having been bottom of the table after losing their first five games -- the worst start to a season in the club's history -- the result left Schalke eighth and unbeaten in their last 11 games in all competitions.
"It's the first time we have turned things around after going behind and we haven't lost for a while now," Choupo-Moting told Sky.
Markus Weinzierl's side will face a stern test of their renewed form when they visit Bundesliga leaders Leipzig, who won 4-1 at Freiburg on Friday to stay three points clear of Bayern, next weekend.
Cameroon's Choupo-Moting showed his class by redeeming himself for a missed first-half penalty.
After setting up Schalke's equaliser in the opening period, the 27-year-old made it 2-1 midway through the second half before Alessandro Schoepf grabbed their third on 90 minutes.
Darmstadt took the lead at Schalke's Veltins Arena when midfielder Marcel Heller poached the opening goal with just six minutes gone.
But Schalke roared back with the equaliser when Darmstadt lost the ball on the edge of their own area and Choupo-Moting fired in a cross which Bosnia defender Sead Kolasinac headed home from close range on 26 minutes.
The hosts should have doubled their tally barely a minute later when Germany international Leon Goretzka was fouled in the area, but Choupo-Moting failed with his penalty attempt.
He fired his spot-kick at the feet of the diving Darmstadt goalkeeper Michael Esser and the ball rebounded to safety.
"I thought he'd dive to the side, so I hit the ball down the middle, but it didn't work the way I wanted it to," Choupo-Moting explained.
"That sort of thing does stay on your mind, but it helps if you score afterwards."
The Cameroon forward then showed lightning reactions to slip his marker when attacking midfielder Max Meyer fired in a cross and Choupo-Moting tapped his shot past Esser on 60 minutes.
It was his third league goal of the season and he could have added another when he fired wide of the post with 14 minutes left.
Austria's Schoepf added Schalke's third with some good finishing after a chip over the Darmstadt defence from Ukraine international Yevhen Konoplyanka just before the final whistle.