The Viola took the lead after a goal by Adrian Mutu, but the visitors from Germany managed to score late on.
Prandelli said: “There was a bit of bad luck, of naïveté and lack of organisation. In that period of the match we were tired and leading, so we should have been more organised.
“It’s a shame, as I think we played a fine game and came close to doubling our advantage at least twice. This is our path with players who need to gain experience and we will continue our work.
“We used up a lot of energy doubling up on their players and keeping the team tight. This is why at that stage we should’ve been more organised to make up for the lack of pace.
“When facing great clubs if you sit back then that makes you vulnerable. We made Bayern run and kept them busy, unfortunately we didn’t manage it for the entire 90 minutes.”
