First-half goals from Adam Maher and Georginio Wijnaldum put the Dutch into a commanding lead in the European U21 Championship Group B clash in Petah Tikva, but they were pegged back immediately after the break by a Sebastian Rudy penalty.
Germany hit the woodwork through Kevin Volland before Lewis Holtby equalised with a low 20-yard drive. However, Fer's late header from a corner gave the Jong Oranje all three points.
Tottenham Hotspur midfielder Holtby captained Germany, while reported Arsenal target Matthias Ginter lined up in central defence.
The Freiburg teenager was not the only Premier League transfer target on show, however.
PSV Eindhoven's Kevin Strootman and Vitesse's Marco van Ginkel - interesting Manchester United and Chelsea respectively - both started in Holland's midfield.
England U21 head coach Stuart Pearce and his assistant Phil Neville were both in the stands at HaMoshava to watch the game, along with a sizeable contingent of Oranje fans from the Netherlands.
Germany fell behind on 24 minutes when Ola John slipped a pass inside from the left and Maher struck home a firm, low shot, with Bernd Leno wrong-footed.
Holland doubled their lead before the break, Wijnaldum making a surging run infield off the right flank and unleashing a fierce shot from the edge of the box. Leno got a hand to the drive but could not prevent the ball bouncing over the line.
Germany pulled a goal back shortly after the break as Holtby broke into the area and was brought down by Jeroen Zoet. Rudy confidently stuck away the spot-kick.
The goal gave Germany an obvious confidence boost, and with Holtby orchestrating their attacks, substitute Volland was unfortunate to see his rasping drive bounce down off the crossbar and hit Zoet on the back.
Florian Jozefzoon was thwarted by Leno when he was put through one-on-one in the 70th minute. But with Germany continuing to push forward, skipper Holtby levelled the match with a strong shot from 20 yards after coming inside from the left channel.
However, Fer would have the final word. After Tony Jantschke had made a saving tackle, the powerful midfielder rose highest to head home the resulting van Ginkel set-piece and seal the points for the Dutch.
They play Russia on Sunday, when Germany take on Spain.