Despite enjoying the better of the opening half-hour, Virgil van Dijk’s close-range header after Ryan Babel’s effort had come back off the crossbar paved the way for a record-breaking 3-0 Dutch win.
Late second-half goals from Memphis Depay and Van Dijk’s Liverpool team-mate Georginio Wijnaldum registered Holland’s biggest win over their neighbours and a first in a competitive match since 1992.
It also meant Germany have gone three competitive matches without scoring for the first time in their history and are winless after two Nations League matches.
“We played very well at the beginning, created many chances, let them run without the ball and did everything we wanted to,” said Werner.
“Then there is this corner which hits the bar and is then turned in. That was a punch in our stomach.
“We missed out on scoring when we had the chances to do so. That’s our biggest shortcoming.”
Manager Joachim Low, who surpassed Sepp Herberger to set a new record in his 168th game in charge of the national team, admits confidence is a problem after six defeats in 10 matches.
“It’s not only about converting the chances. We played OK until we conceded and did not use our chances,” he told a press conference.
“After conceding, you could see that recent results have led to a lack of confidence.
“Why are we not scoring? That’s difficult to answer, we have clear chances.
“Had we lost 1-0, it would have been acceptable but breaking apart like this in the last 10 minutes is not good.”
Lack of confidence is not an issue for Holland, according to boss Ronald Koeman
“This gives us a lot of confidence for the future. We can be really proud, there has been incredible fight and we have shown that we can play great football,” he told Dutch broadcaster NOS.
“I really see a great future for Dutch football. Everyone needed this, not only the national coach and the players, but the whole of Holland.”