The division's bottom side had looked destined for a return to the second tier throughout the entire campaign, having been rooted to the foot of the table since the third match of the season - thanks in part to a three-point deduction.
Osman Zeki Korkmaz's side delayed the inevitable last weekend with a surprise 3-0 away victory over fellow relegation battlers Hatayspor - just their fourth league win of the season and a first in 11 games.
However, they were still in must-win territory heading into Saturday's showdown with Karagumruk, whose own survival is also hanging by a thread heading into the closing stages of the season.
Any dropped points for Istanbulspor would have confirmed their demotion, and their goal lived a charmed life in the first half, with Marcao seeing a goal disallowed and also missing a penalty deep into first-half stoppage time.
Incredible late drama confirms Istanbulspor's inevitable relegation
It looked as though their mathematical lifeline might last at least another day when they then took the lead in the 85th minute, with Racine Coly giving them a late advantage.
However, Guven Yalcin responded within a minute to equalise for Karagumruk, before the visitors were awarded a penalty deep into stoppage time which Sofiane Feghouli converted to win the match in the 97th minute.
The result rubber-stamped Istanbulspor's relegation after two years in the top flight, with their survival in the earthquake-disrupted 2022-23 campaign already considered a major achievement.
The capital outfit have won just four games and drawn seven in the league this season, scoring the fewest goals and conceding the second-most en route to a paltry 16-point tally, including their deduction.
While the home side's fate has now been determined, for Karagumruk the win is a crucial one in their battle against the drop, lifting them out of the relegation zone temporarily.
However, while they are currently above 17th-placed Hatayspor, also on 33 points, should everything remain the same at the end of the season then they would finish the wrong side of the dotted line due to their inferior head-to-head record against the team they are now level on points with.