The young Frenchman headed home Sebastian Giovinco's cross in the dying minutes after Saphir Taider looked to have earned the visitors a point with a thunderous equalizer
After Fabio Quagliarella tapped home from close range to put his side in the lead early in the second half, Saphir Taider's thunderous drive looked to have ensured the Rossblu would depart Turin with a valuable point, and cut the champions' lead at the top to two points in the process.
However, Pogba rose highest to head home Sebastian Giovinco's cross in the dying minutes to ensure the Bianconeri retain their advantage at the top.
Pogba started the match brightly and thought he had given his side the lead after 13 minutes when he nodded home a corner at the far post, but the goal was disallowed after the youngster was unfairly penalized for pushing in the area.
The Frenchman was then cruelly denied once more a few minutes later, as he picked up Isla's pass before rifling a curling left-footed shot from 20 yards which rattled off the post.
Pogba then spurned the best opportunity of the opening 45, directing his header back across goal and out of play after a brilliant delivery from Andrea Pirlo from deep, but that was all the champions could muster as they trudged off the sodden Turin turf at halftime in somewhat frustrated fashion.
It was Bologna, however, who came closest shortly after the break, when Michele Pazienza intercepted a poor pass from Mauricio Isla and rifled a low deflected shot just beyond Gianluigi Buffon's near post.
However, just as it looked like the visitors were growing into the match, the champions finally broke the deadlock. Pogba clipped a clever ball over the top of the defense, allowing Emanuele Giaccherini to square for Fabio Quagliarella to slot home.
Then, out of nothing, Bologna found itself on level terms. Taider picked up the ball to the right of the area and lashed a stunning, swerving strike beyond the despairing reach of Buffon to silence the home support.
The game was suddenly there for the taking. Pirlo swung in another perilous delivery which somehow eluded everyone in the area, before Archimede Morleo upset his teammates by blazing an ambitious effort over the bar when Bologna had men to spare in the Juventus box.
Mikael Antonsson then saved his team with a brilliantly-timed interception as Bendtner looked destined to tap his side back into the lead from point-blank range, before Pirlo bent a curling effort just over the crossbar.
Bologna had everyone behind the ball and looked to have held on for an important point until the second minute of injury time, when Pogba headed home the winner. After Pirlo's initial free-kick cross was cleared, Giovinco expertly created space on the left and whipped a terrific ball to the far post, where the former Manchester United man rose tallest to head in at close range, with the referee this time allowing the goal to stand.