City had fallen behind to Erik ten Hag's side, with the Premier League champions needing a late Bernardo Silva equaliser to force the game to penalties.
Guardiola's men kept their cool from the spot, with the likes of Erling Haaland, Kevin De Bruyne and Ederson all converting from 12 yards.
But despite the win, Guardiola was left frustrated with the quality of the footballs, which were provided by sportswear manufacturer Mitre.
Speaking after the victory, Guardiola told ITV: "It's like a balloon... I'm sorry they decided to play with the ball but it's not good."
Guardiola's frustrations with the hardware were on show during the fixture, with the Catalan coach visibly annoyed when several passes from his City players were kicked into touch.
Express Sport have contacted Mitre for comment.
The City players, from 12 yards at least, didn't appear to have any issues with the ball, considering they netted all but one of their eight penalties.
Bernardo was the only man to miss for the Blues, who picked up their first Community Shield win since 2019.
Mitre provided the balls for City's Community Shield clash with United. (Image: Getty)
City's players didn't seem to have any problems with the ball from 12 yards out. (Image: Getty)
On the performance of his players, the City manager added: "I enjoyed the season against our rival in Manchester and to start the season with a title is good. We are really pleased.
"We lost a lot of balls. After transitions, they are one of the best teams in the world. They are so dangerous to control. But in the end we did it."
Guardiola continued: "It is nice to play this game because it means you won something in the previous season.
"Now we see how the players come back. The target now is not to win the Premier League, it is 'OK, next game... try and win it'. This is what we have to do."
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Attention will immediately switch to next weekend when City head back to the capital for their opening match of the Premier League season.
Chelsea are the opponents for the recently crowned Community Shield winners - a team City have already beaten in pre-season.
A rampant Haaland netted three for the Etihad Stadium outfit, while talented youngster Oscar Bobb was also on the scoresheet when the two met in the States last week.
After that, City return to Manchester for their first home game of the campaign, welcoming newbies Ipswich Town to the Etihad Stadium.
