Early goals from Raheem Sterling and Gabriel Jesus set up the win over the Serie A leaders at the Etihad Stadium, City's third successive triumph in Group F.
Guardiola had described Napoli as one of the three best footballing sides in Europe ahead of the game and, with that in mind, he was in no doubt of the size of his team's achievement.
Guardiola said: "They are one of the best teams I have ever faced as a professional, as a player, as a trainer. That is why I am so proud with what we have done.
Josep Guardiola, Manager of Manchester City gives his team instructions during the UEFA Champions League group F match between Manchester City and SSC Napoli at Etihad Stadium on October 17, 2017 in Manchester, United Kingdom.
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"You cannot beat Napoli - it is impossible to beat them, if you do make a good performance and we did it. That is why I am so happy. I am pretty sure they are one of the best teams in Europe in this moment."
Sterling and Jesus struck inside the first 13 minutes and City threatened more in a devastating opening half-hour. Kevin De Bruyne hit the bar and Jesus had a shot blocked on the line.
But Napoli then began to settle. Ederson saved a penalty from Dries Mertens as the visitors finished the first half strongly and they pulled one back when Amadou Diawara converted their second spot-kick of the game.
Ederson of Manchester City saves a penalty from Dries Mertens of SSC Napoli during the UEFA Champions League group F match between Manchester City and SSC Napoli at Etihad Stadium on October 17, 2017 in Manchester, United Kingdom. (Photo by Stu Forster/Ge
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City did have further opportunities but were ultimately relieved to hang on.
Speaking at his post-match press conference, Guardiola said: "I didn't expect to control for 90 minutes because Napoli are an exceptional team. We made a good first half, for 30-35 mintues. We scored the two goals, we started really good, we could have made a third or a fourth.
"After that when we were a bit tired we were not able to finish our counter-attacks. We arrived late for our pressing and they have a big ability to make short passes inside and outside."
Manchester City's Spanish manager Pep Guardiola shouts instructions to his players from the touchline during the UEFA Champions League Group F football match between Manchester City and Napoli at the Etihad Stadium in Manchester, north west England, on Oc
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City's victory came without striker Sergio Aguero, who was again an unused substitute after making a quick recovery from a broken rib. Guardiola said he would feature "very soon".
Napoli coach Maurizio Sarri said: "We managed to fight back and not many teams at the moment are able to come back in the way we did and cause difficulties for Man City.
"We regret the fact we missed the first penalty, but we know now that we are on the right path to be competitive in Europe."
Asked after the game if he felt City were now on a level with the Spanish giants and were capable of winning the tournament, Sarri said: "Yes, I think so.
Maurizio Sarri, manager of SSC Napoli reacts during the UEFA Champions League group F match between Manchester City and SSC Napoli at Etihad Stadium on October 17, 2017 in Manchester, United Kingdom.
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"They are an extraordinary squad. They have tremendous physical, technical and tactical qualities and if they can maintain their physical shape they could go all the way," he added.
City have now won 10 in succession in all competitions but defender John Stones felt this one had required a real show of mettle.
Stones told BT Sport: "I think tonight was a great test to see where we were really at after a good run of hard games. We knew it was going to be a tough test."
City now have a six-point advantage over Napoli, the side expected to be their toughest challengers in the group. They face each other again in Italy in a fortnight.
Additional reporting via Reuters.
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