Antonio Conte's side came into the match knowing victory would confirm a top-four finish with two Serie A games remaining, but Jonathan Rowe's stoppage-time winner left Napoli still nervously looking over their shoulder in the race for Europe.
Bologna stunned the home crowd after just 10 minutes when Federico Bernardeschi fired a powerful strike into the top corner after being picked out by Juan Miranda. The visitors nearly doubled their lead moments later when Miranda struck the woodwork as Napoli struggled to settle.
Napoli slowly improved and Scott McTominay came close to equalising with a header from a corner that drifted narrowly wide. However, Bologna struck again in the 34th minute after VAR awarded a penalty for Giovanni Di Lorenzo's foul on Miranda. Riccardo Orsolini converted calmly from the spot to make it 2-0.
Napoli responded before half-time when captain Giovanni Di Lorenzo reacted quickest inside the area to score from close range and give the hosts hope heading into the break.
Conte's side returned with renewed energy and levelled only three minutes into the second half. Rasmus Hojlund created the opening with a clever pass and Brazilian midfielder Alisson Santos finished smartly to spark celebrations around the stadium.
Napoli pushed hard for a winner, but Bologna delivered the decisive blow in stoppage time when Jonathan Rowe produced an acrobatic finish to seal a dramatic away victory.
After the match, Conte admitted his team's slow starts were becoming a serious concern.
"When you press, you've got to do it properly," Conte told DAZN Italia. "If you only do it half-way, then you just end up running around for nothing.
"It wasn't the first time this season we were 2-0 down, so it is evidently not a fluke. We need to be more determined in our approach because it keeps happening."
Conte felt Napoli deserved more after their second-half response but admitted his side had to learn how to protect results.
"We managed to get it back on track and tried to win, but if you can't win, then at least try not to lose," he said. "I don't think we deserved to lose, but these things happen."
The Napoli coach also praised Hojlund's work rate after the striker again led the line on his own.
"Let us not forget, he is the only striker we've got right now," Conte added. "He works hard for the team and still has a lot of room for improvement."
Conte also highlighted the progress of Alisson Santos, who impressed throughout the second half with his direct running and attacking threat.
"Alisson is improving a lot," said Conte. "We are trying to use him in a way that suits his characteristics. He needed time, but he has improved greatly."
The defeat has left Napoli still fighting for a Champions League place with two matches remaining, while Bologna climbed to eighth place after one of their biggest wins of the season.
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