A scrappy Leroy Sane goal late in the first-half eased any tension building in the City end.
Sergio Aguero then stretched the aggregate lead to 4-1 with his 23rd goal of the season.
However, in typical City fashion, Kevin De Bruyne then went up the park only a minute later to score the winner.
Speaking after the game, Guardiola said: "We are so happy to be there, to reach this final. We played an amazing game until 2-0 and then we lost control, these type of games never end until the end. This is a lesson for next weekend in Cardiff in the FA Cup and especially for the Champions League.
"At 2-0 we knew it would be easier because they needed three or four goals but with one minute left it was 2-2 and anything could happen.
"It's not for me, it's for Manchester City, a club who are trying to reach another level. We try to keep going, the important thing for me is to be there. We try to keep going in the FA Cup, in the Prenier League.