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 equaliser
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.
The hosts named a much-changed line-up from the weekend win over Catania, as Mirko Vucinic, Arturo Vidal, Stephan Lichsteiner and Kwadwo Asamoah all missed out on a starting berth, while Pogba and Nicklas Bendtner retained their places in the side.
For Bologna, Panagiotis Kone and Frederik Sorensen came in to the side which lost 3-1 to Inter at the weekend, while Alessandro Diamanti missed out.
Juventus, as expected, controlled the early pace of the game and forced Federico Agliardi into a couple of early saves with efforts from distance.
Pogba in particular 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 penalised 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.
As the half wore on, Juventus were unable to carve out many meaningful opportunities despite their dominance of possession, with a 30-yard dipping shot from Bendtner the only effort of note from the striker around the half-hour mark.
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 half-time 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 defence, allowing Emanuele Giaccherini to square for Quagliarella to slot home.
Just a few moments later, the Italy veteran almost doubled his tally, but Agliardi was equal to his fierce effort on the half-volley following Bentdner's pass.
With Bologna now forced to abandon their defensive approach, the space began to open up for the Bianconeri. Quagliarella almost made this space count when he drifted infield and clipped over the top for Bendtner, but the Denmark striker could not quite get a toe on the ball.
Then, out of nothing, Bologna found themselves in 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 team-mates 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.
Juventus piled on the presure, with substitute Sebastian Giovinco twice coming close with right-footed curlers from inside the box, before Bendtner fired wired.
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.