Koulibaly scored in the last minute to give Napoli an important victory over their rivals on Sunday to cut the gap at the top of the table to just one point with four games remaining.
Juventus arguably have the trickier run-in of the two sides, having to play both Inter and Roma in the league, as well as a Coppa Italia final with AC Milan in between, and it is that Derby d'Italia with Inter which Allegri believes will be the decisive point in the title race.
"It was a very bad match for both teams, with practically zero shots on goal. We did what we could and come the end it looked like we would have to draw," the Italian said after the 1-0 defeat.
"Unfortunately we did not mark properly for their corner and so we conceded a goal. It was a head-to-head clash and Napoli did what they had to do, they kept the ball better and so congratulations to them for that.
"Now, for us, Saturday's match against Inter is the really decisive one. We still lead the championship, we have two games at home and two away, but the decisive one will be in Milan.
He concluded: "Now we have to get over this defeat and get back to work immediately."