Despite making a fast start in north London, the Sky Blues looked off pace against Nuno Espirito Santo's side for a large chunk for the clash, with a second-half strike from Heung-Min Son enough to seal the three points for the hosts.
Several first-team regulars were left on bench having returned to training during the past week following their involvement in the European Championships and Copa America.
As the game approached full-time, Gündoğan seemed to appear in a state of pain as the German international leapt to the floor after receiving contact in his own half with City trying to pull an equaliser, following which the referee blew the full-time whistle.
Speaking in his post-match press-conference, Guardiola confirmed that the 30-year-old suffered a shoulder injury, whose extent remains unknown, and will be assessed by the club staff on Monday, according to Sam Lee of The Athletic.
Additionally, the Catalan manager spoke about De Bruyne's performance off the bench, as the Belgium international was called on to try and affect proceedings during the final stages of the tie.
The star midfielder suffered an ankle injury on international duty this summer, but managed to create a series of openings for his side after replacing Riyad Mahrez on the 79th minute, despite only returning recently to pre-season training.
Guardiola added: "Kevin (De Bruyne) didn’t do one training session so far due to his ankle. Kyle (Walker), John (Stones), Aymeric (Laporte) came back well. The guys who have been here from the beginning deserve to play. We have to continue working."
The defeat to Nuno Espirito Santo's side at the weekend means that Guardiola's side have suffered consecutive 1-0 losses since the start of the 2021/22 campaign.
After making a slow start to the fresh campaign, the Manchester outfit will be looking to get up and running and avoid a repeat of their showings at this stage from a year ago, when they slipped to the bottom half of the table by making a disastrous start to the new season.
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