After taking a first half lead, the Boys in Blue were pegged back deep into stoppage time by Portland Timbers to force extra time in Sunday's MLS showpiece.
But with the showpiece still level at 1-1 after 120 minutes, Ronny Deila's side rallied to win 4-2 on penalties and become champions for the very first time.
Asked for his thoughts on an historic day in NYCFC’s and the City Football Group's history, Guardiola said: “I was really impressed with how they handled extra time.
“When you concede a goal with 10 seconds left to finish the game to be champions in extra time you can be destroyed.
“In extra time, wow, they were much, much better and it means how strong they are these players and the manager.
“And after, the penalties, the goalkeeper (Sean) Johnson made some incredible saves.
“It’s a huge compliment for the organisation, for New York City because it’s the first time (as MLS champions) and always the first time is special.”
MLS Golden Boot winner Valentin Castellanos had handed NYCFC the advantage at Providence Park when he headed home impressively on the stroke of half-time.
It was his 23rd strike of a hugely productive season, and Guardiola says the Argentine is capable of being a success in European football.
“I think he’s a guy who will do the next step in Europe,” the City boss said of Castellanos.
“What I saw when the scouting department talked to me and (former City assistant and NYCFC boss) Domenec Torrent, when I was there, and Dom was there we talked about him.
“I know he has the quality and I think he is ready to make the step to Europe, we will see where.”
Hear Pep Guardiola's press conference in full via the video above...