The German giants edged the English champions thanks to a late strike from ex-City defender Jerome Boateng in their Group E Champions League opener and the result pleased Guardiola who felt his players were the better set of the two at the Allianz Arena.
"They played better for the first 20 minutes and we played better for the rest of the game," he told Sky Sports 5HD.
"We deserved this victory. In the second half we played at a very high level."
The former Barcelona boss added that he was delighted to see his team rewarded ahead of a hectic schedule while touching on the fitness of Brazilian defender Rafinha who has been sidelined with an ankle injury for more than a month.
"We can't forget against which team we played tonight and I'm happy with the rest because it is the first game in (a busy) two months," Guardiola added.
"It was Rafinha's first game in two months. He had been out injured so he played with a big heart and the rest of the players played at a good level."
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