He is mainly remembered for his assassination in Paris in 1938 by a Polish Jewish teenager, Herschel Grynszpan, which provided a pretext for Kristallnacht, "The Night of Broken Glass" on 9–10 November 1938.

[3][4][5] Adolf Hitler himself sent his two best doctors, personal physician Karl Brandt and surgeon Georg Magnus, to Paris to try to save vom Rath's life.

Hitler promoted him to the rank of Legal Consul, First Class (Gesandtschaftsrat I. Klasse), hours before vom Rath's death on 9 November at 17:30 (5:30 p.m.).

The records were falsified in 1942, and the Germans spread propaganda that Grynszpan's intention was to kill the Nazi ambassador, Count Johannes von Welczeck.

"[9] American journalist Dorothy Thompson reported widely on the case and raised funds for Grynszpan's defence in his French trial, which never took place.

Under French law, those convicted of murder for political reasons faced the death penalty, but who committed a crime passionnel were usually given a lesser sentence.

[11] He was sent to the Sachsenhausen concentration camp to face a trial there, one that Joseph Goebbels planned to turn into Nazi propaganda about an international Jewish conspiracy and to claim it as evidence that Jews had started World War II.

By 1941, various sources had made both the Ministry of Justice and the Reich Security Main Office aware that Ernst vom Rath was apparently active in Paris’s homosexual circles and had likely met Herschel Grynszpan there.

[17][18] In 2001, Professor Hans-Jürgen Döscher alleged in his upcoming book, Reichskristallnacht, that Vom Rath was nicknamed "Mrs Ambassador" and "Notre Dame de Paris" as a result of his homosexual activities.