The home crowd were in fine voice at the start of the contest, but were stunned into silence with just 10 minutes on the clock.
After receiving a pass inside the box from Juan Miranda, Federico Bernardeschi produced a rocket of an effort that found the top corner to give the visitors the lead and secure his third Serie A goal of the season.
Antonio Conte’s side almost found themselves in an even worse position just two minutes later, when a shot from Miranda struck the woodwork.
The Azzurri finally began to stir into life and Scott McTominay will certainly feel like he should have equalised on the half-hour mark, as he steered a header narrowly wide of the target from a great position following a corner-kick.
Just as it looked like Napoli were getting themselves back into contention, the Rossoblù doubled their advantage from the penalty spot after 34 minutes.
Following VAR intervention, the referee eventually awarded a spot-kick after Miranda was fouled by Giovanni Di Lorenzo, and Riccardo Orsolini duly converted from 12 yards out to net Bologna’s second goal of the evening.
But the action didn’t end there before the interval, as Di Lorenzo took advantage of some static Rossoblu defending to rifle the ball home from close-range and halve the deficit in stoppage time.
Conte’s half-time team talk must have been an inspiring one as Rasmus Hojlund picked out Alisson Santos and the Brazilian attacking midfielder’s smart finish levelled the match just three minutes after the restart to send the home support wild.
After such a bright start to the match for Vincenzo Italiano’s team, the momentum was now fully behind last season’s Serie A champions.
However, with full-time in sight, Bologna grabbed a dramatic winner in stoppage time thanks to a superb acrobatic finish from Jonathan Rowe.
With so much at stake in the final straight of the season, second-placed Napoli sit three points clear of fifth-placed AS Roma with two matches remaining, and the Azzurri will be desperate to return to winning ways in their next game away at already-relegated Pisa on Sunday. Meanwhile, a win sees Bologna move up two positions to eighth in the Serie A table.
Flashscore Man of the Match: Alisson Santos (Napoli)