The FDJ sprinter claimed his maiden Grand Tour stage at the end of a 112km dash from Giovinazzo marred by three crashes inside the last two kilometres as the road was made slippery by rain.
The first 100 kilometres had been neutralised by the peloton in protest against the bad road conditions in southern Italy, and the real action started only in the finale, with Bouhanni suffering a puncture before being helped back into the bunch by his team mates.
Bouhanni lost considerable ground some two kilometres from the line but fought his way back to outsprint Italian Giacomo Nizzolo.
"I suffered a puncture on the front wheel and had a problem with the rear wheel but my team mates were fantastic in pulling me back towards the front of the peloton," said Bouhanni.
"In the last lap I slipped twice or three times but managed to stay on the bike and then I gave everything."
Tom Veelers of the Netherlands came home third as Australian Michael Matthews retained the overall leader's pink jersey.
German Marcel Kittel, who won the second and third stages and was favourite for Tuesday's ride to Bari, pulled out with a fever.
"Unfortunately Marcel Kittel will not start the fourth stage of the Giro today due to fever," his Giant Shimano team said on their Twitter feed.
(Writing by Julien Pretot; Editing by Ed Osmond)
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