Jesus put the Premier League leaders ahead inside eight minutes but the Swiss champions responded to take victory on the night with goals from the impressive Mohamed Elyounoussi and Michael Lang.
When asked about the ribbon he said: "If one day in prison was already too much, look how many days they've been there now".
"It's good for the rhythm of the future".
Guardiola will have a clearer picture of the title race after Saturday's lunchtime clash between nearest rivals Manchester United and Liverpool.
"It's special for us to beat this team and we go out of the Champions League with a decent performance in a very hard situation", said Basel coach Raphael Wicky. "He has to grow up and be stronger, but the huge quality is there".
Even with the poor performance of the side, and poor result, there were some positives from the game.
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City completed 977 passes to their opponents 249, but Guardiola said they lacked a goal and appeared to be passing for the sake of it.
"Just passing the ball without any movement, to just pass and pass for the sake of it is nothing".
He added: "It's not easy to play when the first leg was 0-4". We spoke about that and in the first half. We created a lot of chances in the first half, but after 1-1 in the second half, the best way is to create the passes in the build-up to run in behind.
"But, after 1-1 in the second half, it didn't happen". Just to pass to pass for itself is nothing. I think there's a really good spirit there, that they want to climb the table, and overall we've only been beaten once in six. We just passed for ourselves and that is not football.
"I'm really happy and proud". Portal "WhoScored" for uncertain defensive set Zinchenko worst rating in the team - 5,9 points. We can be very proud. At Bayern Munich in three years, he won the Bundesliga everytime, two German Cups, one UEFA Super Cup and one FIFA Club World Cup.
"They have showed that for months in all competitions".
"We have training sessions to decide before the game".