It is the City's first defeat in 227 days in all the competitions.
Manchester-born defender Tosin Adarabioyo also started while Spanish forward Brahim Diaz made a lively appearance as a 62nd-minute substitute.
"We lose a game, it's part of our profession", Guardiola said.
"We know Man United have a very good team as well but we will play our game and try to control the match, to be better than them and bring the three points back home". People say things when you win a lot and you can forget that now. "I think we did that well and they did not threaten as they normally would".
City were awarded a penalty in stoppage time that was converted by Aguero, but it was too little too late to save their flawless record.
City keeper Ederson gifted Shakhtar a second as Ismaily took advantage to tighten the Ukrainian champions' grip on a knockout-stage berth before Sergio Aguero blasted a late penalty for the visitors.
"It's how they arrive in the moment on that day".
"Maybe you are good today but in February, you're a disaster. It won't be easy".
The match was fairly meaningless for City, with top spot already secured, and focus can now turn to Sunday's Manchester derby against United at Old Trafford.
The first team is set to remain in Ukraine on Wednesday night before flying back to Manchester on Thursday after a light training session in Kharkiv.
"You can not expect and all the season I've said many times, we are not going to win all the games".
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