First-half goals from Saints pair Sekou Mara and Moussa Djenepo stunned the eight-time winners on an extraordinary evening at St Mary’s.
But, unlike on Sunday when the influential pair were not required in a thumping 4-0 FA Cup victory over Chelsea, the decision backfired as they were unable to prevent City suffering elimination after coming off the bench in the second period.
Manager Guardiola felt his Premier League champions were destined to struggle on the south coast regardless of the team he picked.
He said: “Who knows whether with Kevin and Erling it would have been different? I don’t know it.
“We tried to do our best and we rotate the team when we played against Chelsea after the Premier League and it’s good.
“I understand how this business works. Always we try to have everybody involved and everybody has to do it but today was not the case.
“I had the feeling today it doesn’t matter what line-up I am selecting, we are performing this way. Don’t ask me why. This is my experience.
“It doesn’t matter today the line-up we choose, it would happen because we were not here. And that’s why when this happen, they deserve it.”
City began the match as strong favourites but failed to register an attempt on target across the 90 minutes.
Battling underdogs Southampton will face Newcastle in their first League Cup semi-final since going on to finish runners-up in 2017.
“The best team won,” continued Guardiola. “They were better. We had a bad night and we didn’t play good.
“We didn’t perform well and to win games – I’m not talking titles – you have to deserve it.
“When I win something I want to deserve it and today was not the case, that’s why Southampton deserve to be in the semi-finals.
“Today was not even close to what we are.”
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