After a speeding violation forced the car he shared with Kevin Estre, Fred Makowiecki and Michael Christensen to start from the back of the GT3 field, Vanthoor was fighting over third place with his younger brother Dries Vanthoor's Phoenix Audi.
The pair duelled on the long Dottinger Hohe straight and continued to run side-by-side approaching the Tiergarten, with the Audi slightly ahead, where light contact between the Porsche's right front and the Audi's left rear unsettled the #1 car and sent it into a spin.
Laurens Vanthoor managed to avoid the armco on the left, but had a hard impact with the barrier on the right-hand side as the track curves left before the Hohenrain chicane.
The accident put the #1 out of the race, while Vanthoor was able to extricate himself from the car and made a precautionary visit to the medical centre. The track marshals stationed behind the barriers Vanthoor hit also escaped without injury.
Dries Vanthoor said: "We already know from each other that we don't want that. We have to look again at what happened.
"We were side by side and I was out in the left-hand corner and he was out in the right-hand corner. When you see something like that: It's nobody's fault.
"It's super-shitty that he's out now because of something like that. I don't think that either of us did anything wrong or was aggressive.
"Things like that happen and it sucks when it's your own brother."
Laurens said: "I was driving side by side with the other car, then we ran out of space.
"We only touched slightly, but the hit on my car was probably in the most unfortunate place.
"I spun at high speed - that was it. I'm fine. But it's incredibly unfortunate for the whole team."
Porsche Motorsport boss Thomas Laudenbach commented: "It wouldn't be fair to pass judgement now.
"They touched several times, it was close. We have to look at that calmly. Honestly, the most important thing is that Laurens is okay. That was a heavy impact."
The car had briefly led in the opening phases in the hands of Kevin Estre, following a spin for Nicki Thiim's TF Sport Aston Martin.
Several fancied GT3 contenders have also fallen by the wayside, with the polesitting Octane126 Ferrari delayed by a puncture while Simon Trummer was at the wheel and the #72 RMG-run BMW Junior Team M4 losing time in the pits after Daniel Harper collided with the Adrenalin BMW #331 in the Hohenrain chicane.
The #27 Toksport-WRT Porsche had also retired after contact at the NGK Chicane between Julien Andlauer and the #99 Rowe Racing BMW of Nick Yelloly, which had been qualified second by Augusto Farfus.
Both cars were heavily damaged afterwards, with Yelloly earning a penalty as a result.
Andlauer told Autosport's German language sister site Motorsport-Total: "It was a pretty big accident and it was over for us.
"I can't say more than sorry for the guys, I couldn't avoid the contact that came from way behind."
But Rowe team boss Hans-Peter Naundorf said: "We have watched the videos several times and it is incomprehensible to me how our car can be penalised. The track was wide enough."
