City scored three times in the last 19 minutes on Tuesday to win the first leg of their last-16 tie 5-3 at the Etihad Stadium.
Fabinho produced an impressive performance, setting up both Radamel Falcao's header and Kylian Mbappe's fine strike for the visitors.
But he felt Guardiola's strategy ensured Monaco had to work so hard throughout the game that they were physically spent come the final minutes.
"They put in place a scheme to destroy our 4-4-2," the 23-year-old told reporters.
"We had to be moving all the time to block the spaces – it was difficult. It was physically hard.
"Personally, I suffered in the last 10 minutes – but that is not why we lost. Perhaps it was because we lacked the experience.
"When we conceded the third goal, we conceded to attack. We did not think about the return match. We lost 5-3 and could have even lost 6-3 – we have to learn from these games."
Fabinho, though, has not lost hope that Monaco can progress when the two teams meet in next month's second leg.
"It is still possible to qualify," he said. "It was a very balanced match and we mostly conceded goals on our mistakes.
"At home it is going to be different. We will play in front of our supporters and I hope that we will remember the mistakes we made here so we do not reproduce them.
"Kylian brought us a lot of speed. He could have even scored a second goal on an individual action. He must get used to playing in major games like this.
"Falcao is a very important player for the team. He scored twice and would have had more without a great goalkeeper [Willy Caballero] who had an extraordinary reflex save with his foot late in the game."