Special labs in Sweden and France found the Soviet nerve agent was used to poison the Russian opposition leader, a spokesperson for the German government said.
Mr Navalny, an outspoken critic of Vladimir Putin, is being treated at a Berlin hospital after falling ill last month during a domestic flight in Russia.
Samples taken from him have also been sent to the Organisation for the Prevention of Chemical Weapons (OPCW) in The Hague for tests.
"Independently of the OPCW's investigations, three laboratories have now independently identified a military nerve agent as the cause of Mr Navalny's poisoning," German government spokesman Steffen Seibert said. "We renew our call for Russia to explain these events."
Army doctors at Berlin's Charite hospital were the first to say Mr Navalny - who awoke from a coma last week - had been poisoned with novichok.
Russia said it has seen no evidence that Mr Navalny was poisoned.
The 44-year-old Russian dissident is said to be responding to speech.
Germany has said the poisoning of Mr Navalny was an attempt to kill him and has threatened to abandon a joint underwater gas pipeline project with Russia if Moscow fails to cooperate with the investigation.