The former Brentford No1 kept a clean sheet as Bayer won 2-0 and admits seeing City manager Pep Guardiola ring the changes gave the visitors a confidece boost.
After being named man-of-the-match, Flekken said: "It was definitely a difficult game, and the preparation was definitely different when we heard there were so many changes in their starting 11.
"Also, it offered us an opportunity, of course, and we went open-minded into the game with the belief that we would get something out of it.
"The team played a magnificent match, and I'm able to say we deserved the three points. Their team was definitely a surprise, but we had that same kind of surprise against Bayern in the Bundesliga, and that was the game we made the mistake of being too passive in defence and not being brave enough with the ball. We learnt from that game, and today was completely different."
He added, "We were brave enough to play forward and play in our own style. I think that was the most important thing - we stayed true to ourselves.
"The defensive urgency was key today. Making those runs back, getting back and trying to block every shot on target – and that happened a lot, especially in the second half."
On the clean sheet, Flekken also said: "If you can grow into the match save after save as a goalkeeper, at some point you really get that feeling that 'nothing's going to happen today' and you can master every ball that comes towards your goal.
"And that was exactly what happened. It's wonderful to have a game like this, but it wasn't just me; it was the whole team who played a terrific match, and we are delighted to take the three points home with us."