The Azzurri closed the gap at the top of the table to just one point with four rounds to go thanks to Kalidou Khoulibay's winner.
"It was a terrible game from both teams. There were barely any shots on goal. We had some difficulties, but we should've taken it to the end more carefully rather than allow a goal from a set play," Allegri told Mediaset Premium.
“It's a head-to-head and anything can happen in those situations. Now we have a rest day, then have to prepare for what I think really will be the decisive match for our season against Inter.
“We are still top of the table, we still have the advantage. There are four games to go, two at home and two away, so we'll see what happens.
“Napoli deserve some credit for their victory, but there were barely any chances. They had to win, we needed to either win or not lose.
“There is another advantage, as goal difference is in our favour and the head-to-head record is even. We have to shake off this match, get ready for the next and that will be very important.
“Napoli did well in their pressing tonight, we were less good in our control of the ball. I told the lads we have to shake this off in a couple of days, because I think the Inter game will be decisive for our campaign."
Paulo Dybala was replaced by Juan Cuadrado at half-time after another disappointing performance.
“I only replaced Dybala because I needed more coverage and physicality on the wings. That's also why Mario Mandzukic came on.
“Napoli deserve some credit. It was a head-to-head that was decided by a single incident. Napoli kept possession, as they're good at that, and we weren't as sharp as usual on the counter. They deserve some credit, but we have to focus on the next match."