Erling Haaland hit the winner on five minutes, with Guardiola admitting Saints pushed them all game.
He said afterwards: "Today it was not how they defend deep it was how good they play with the ball with the keeper and the movement. It's a good game to learn as a manager. I am going to learn a lot with Russell (Martin) because they did really well. We were humble and accepted that they did really well. Last two games, Wolves and Southampton, are at the bottom of the league and if this is the level that shows how tough this Premier League is.
"They played really good. They didn't create many chances but it was an incredible effort to get the ball from us. We created chances that we couldn't convert but the result is good.
"The build-up is exceptional. They open the channels. They link well with the striker and every moment makes sense. I knew after what people had said to me about Russell and we tasted it today. The players were not bad, they were good. When a team plays that level you have to accept it.
"Important thing is being there. We created chances, as always Erling had two or three clear ones. But I'm not concerned, it's important to have 23 points now.
"Most of the teams defend so deep. Now we will play Spurs, Bournemouth and Brighton and they won't defend deep. So we have to adapt now. But lately a lot of defences sit so deep. We did create spaces to create, Savinho was really good today.
"We have just two or three days to recover now. We are used to playing during 11 months every three or four days. The issue is that we can't rest some players but hopefully sooner or later we can rest some and some can come back."