Michael O’Neill admitted three key minutes really hurt his side as he suffered his heaviest loss as Northern Ireland manager.
A hat-trick from Serge Gnabry saw Germany claim a 6-1 win in the final group qualifier.
On a tough night in Frankfurt, Northern Ireland were a minute from going in level at 1-1 at the break.
But a goal from Leon Goretzka put the Germans in front, before Gnabry made it 3-1 90 seconds into the second half, killing the game.
O’Neill said: “It was a tough night, when you come into a game like this and you are missing players, at the back of your mind you fear this might happen, and unfortunately it did.
“We couldn’t have got off to a better start, to be honest - great goal, we’d some good pockets of play in the first half.
“We had to defend deep, and we knew we’d have to defend deep.
“I think the killer really is the fact that we were a minute from going in at half-time at 1-1 and, after 47 minutes, we are 3-1 down.
“That is down to the quality of the opposition and down, at times, to a little bit of poor defending on our part.”
Michael Smith had given Northern Ireland a seventh minute lead, but the Germans levelled 12 minutes later through ex-Arsenal and West Brom player Gnabry.
Goretzka made it 2-1, before Gnabry added two more to seal his hat-trick.
Further goals from Goretzka and Julian Brandt rounded off a comprehensive win for Germany, who finish as group winners.
Northern Ireland, who finish third behind the Netherlands, now face a play-off with Bosnia in March.
O’Neill, who was without several key players last night, including Jonny Evans and Jamal Lewis, was realistic about the result.
“Tonight we saw aspects of a German team that is progressing very, very quickly,” he added.
“You look at people like Gnabry, I thought he was unplayable tonight - fantastic movement, fantastic finishes.
“For us, a double header against the Netherlands and Germany, and not a full-strength squad, we just don’t have the depth to be able to deal with that.”
O'Neill was also satisfied with how they coped in a tough group.
"Thirteen points is no shame for us in a group with the quality of Germany and Holland in it.
"For many of our players this is their first campaign and they can learn from nights like this.
"It was very difficult for us to come here and get a result, but equally you never want to be beaten as we were, and beaten 6-1."
O'Neill is convinced his players will learn from this.
He added: "You can't go out every week and play well and the game goes your way, it is about how you react to disappointments and nights like tonight."
O'Neill continued: "Hopefully our players, while they are disappointed by being beaten, and being heavily beaten, hopefully they are inspired by this level.
"Hopefully it gives them the inspiration to make the most of their careers to get the highest level possible, so that if they get the opportunity to come back here again, they are more equipped to deal with it."