The visitor led by two goals after Ilkay Gundogan's penalty and Kai Havertz's expert long-range finish punished the Three Lions.
However, three goals in the space of 12 minutes from Luke Shaw, Mason Mount and Harry Kane had already-relegated England in front with seven minutes to play.
An error from goalkeeper Nick Pope allowed Havertz to make it 3-3 late on, but head coach Flick acknowledged Germany must be better at protecting a lead in Qatar.
"The result is very disappointing. I think we were very stable after 2-0 and we made individual mistakes, and you have to say that England brought in two fresh players who then also played a part in making England more effective offensively," Flick said.
"We made individual mistakes and that's why it's disappointing.
"You have to look at the whole game and I think we did many things well, really well. In a phase where we got the three goals, that shouldn't happen to us, because especially at a World Cup, things like that are of course deadly and you're eliminated faster than you think.
"Therefore, if you look at it positively, you simply have to say that we know what we can work on.
"We'll analyse the game properly again because, of course, at first glance, I've seen the goals conceded, just once or twice now, and that's partly individual, where we sometimes made the mistakes. And everyone has to do their job over 90 minutes and we have to work on that."
Flick, though, was effusive in his praise of Bayern Munich star Jamal Musiala, who was a constant thorn in England's side and drew the foul from Harry Maguire for Germany's opener from the spot.
"Jamal just showed why he is an exceptional talent. He got us the second goal from in his own half and he's both defensive and offensive, I think he's a player that's good for us," Flick added.
"And simply by his dribbling ability, he can pull out situations like penalties, but of course also he can move opponents around, one or two players are out of position and then it's a different situation.
"Then we have more room, more space and those are the things that are good for us."