Summer signing Romelu Lukaku and midfielder Andre Zambo Anguissa scored stoppage-time goals to earn Conte his second victory as Napoli manager and provisionally move to fourth in the standings.
The former Chelsea boss, however, was concerned about not having a squad depth and dealing with last-minute changes to his team as the transfer window closed on Friday.
"We take these three points knowing full well that we have to work after this absurdity of the transfer market," Conte told reporters.
"Coaches have to train players who are going to leave and wait for players we've never worked with and don't know in what condition they'll be when they arrive.
"We had zero midfielders on the bench today, as yesterday (Gennaro) Iaccarino and (Coli) Saco went on loan. We had to pray that nothing happened to (Stanislav) Lobotka and Anguissa.
"I hope that things can change in future, seeing as everyone is ready to change formats and rules."
Conte added he was pleased with Napoli's transfer window despite the failure of Victor Osimhen's move to Saudi Pro League side Al Ahli.
"We did not just bring in players to build on an existing team, but to fill certain empty slots, and I am happy with the work done by the club," he said.
"If we had been able to sell Osimhen, it would've been an even better situation, but what happened cannot be changed and we move on."
