The win was ultimately deserved as, while Palermo started well enough, Bologna had by far the best of the second half following Santiago Garcia’s 57th-minute dismissal after he picked up two yellow cards.
Bologna move to joint-10th while Palermo stay seventh, missing out on the chance to go fifth.
A floodlight failure just after kick off delayed proceedings, with Palermo starting the brightest once matters resumed.
Viviano made an excellent stop when Sinisa Andelkovic was left unmarked at a corner to power a header towards the bottom left as, playing on the break, Palermo posed all the questions.
But later in the first half Bologna started to threaten an end product to their possession, as Diego Perez put Marco Di Vaio’s deflected cross over from close range while Riccardo Meggiorini forced a good stop from Sirigu with a fizzing long-range effort.
It was goalless at the break and, with the second half starting in nondescript fashion, it needed a game-changing moment to spark things back to life.
That came on 57 minutes, when a needless challenge on Meggiorini saw Argentine defender Garcia receive his second yellow card.
With the visitors down to 10 men Bologna looked to make their possession count, as frustrating Uruguayan playmaker Gaston Ramirez put a close-range header wide while Di Vaio fluffed his lines when his header flew off target following a superb Francesco Della Rocca cross.
There was another moment of controversy as Di Vaio tumbled to the deck after going shoulder-to-shoulder with last-man defender Andelkovic but the referee waved play on: had he adjudged it a foul, the Slovene would have walked.
Paponi came on with a quarter of an hour left and almost had an instant impact when he fired a rasping drive just over the bar.
And, with the clock winding down, the former Parma reserve striker snatched the win as he rose impressively to guide a superb header past Sirigu into the top right.