Southampton, who knocked out Arsenal in the previous round and arrived on a 19-game unbeaten run in all competitions, took the lead through Finn Azaz's curling finish with 11 minutes remaining before Jeremy Doku levelled and Nico González struck the winner three minutes from the end.
Guardiola was candid about his decision to start Doku and Savinho on the bench.
"They were 19 games unbeaten, so I never thought it would be easy. The energy we had in the second half from Jeremy and Savinho helped, but if they started from the beginning they would not have this energy. Because Jeremy, especially when you play three days, three days, three days, the risk of getting injured is so massive. The players who started deserved to play, they helped us."
He credited his side's second-half dominance despite the scoreline not reflecting it until late.
"The first half was not bad. We didn't concede much. In the second half, we played at the level we played in Burnley but unfortunately we arrived in the 18-yard box and we were not clinical enough. You have to wait for the holding midfielder to score an outstanding goal. How many times in the second half did Southampton cross the halfway? One. And what a goal."
On the nature of the comeback: "Football is unpredictable. Big credit for the way they defend, the way they play. We create chance after chance after chance. But football is like this. We equalise through the deflection. When you analyse, we created chances — more clear than that. That's football."
Guardiola also singled out Doku for specific praise.
"The way Jeremy grew up in the last two seasons in terms of impact, he is an incredible threat. He is almost impossible when 1 v 1 in the final third."
Manchester City will face either Chelsea or Leeds United in the final. The second semi-final takes place on Sunday.