Neymar set up Marquinhos' equalizer in the 90th minute to cancel out Mario Pasalic's opener, before Eric Maxim Choupo-Moting struck the winner three minutes later.
Atalanta head coach Gasperini praised Neymar's performance at the Estadio da Luz in Lisbon.
PSG waited until the 90th minute to flip the switch 😅 pic.twitter.com/YXe20YjUNR— CBS Sports (@CBSSports) August 12, 2020
"He is a player we paid a lot of attention to, because we saw that as soon as he had a little space, he would become very dangerous," he told a news conference.
"Neymar is a great football player, a crack. And he proved it [again] as well, even though I believe we managed to limit him quite often.
"However, he proved he is a top player."
Kylian Mbappe came off the bench for PSG on his return from an ankle injury and set up Choupo-Moting's winner.
Gasperini said the France international's introduction gave the Ligue 1 champions a huge boost.
"Without any doubt his entrance gave PSG some energy they were losing, at that moment," he said.
"It was definitely a fundamental, important entrance, because of his accelerations and the dangers he caused. However, it seemed that the worst was over, that we had overcome it.
"Therefore, the goal we conceded, the equalizer especially, leaves us with great bitterness."