Mr Navalny, a long-time opponent of Russian President Vladimir Putin, collapsed on a plane on August 20 and was taken to a hospital in the Siberian city of Omsk after the plane made an emergency landing.
Chancellor Angela Merkel’s spokesman, Steffen Seibert, said in a statement on Wednesday that testing by a special German military laboratory had shown proof of “a chemical nerve agent from the Novichok group”.
Toxology tests of blood samples from Mr Navalny produced “unequivocal evidence” that he was poisoned with Novichok, Mr Seibert said.
Novichok, a Soviet-era nerve agent, was used to poison former Russian spy Sergei Skripal and his daughter in Britain.
It is a cholinesterase inhibitor, part of the class of substances that doctors at the Charite initially identified in Mr Navalny.
“The federal government will inform its partners in the EU and NATO of the results of the investigation,” Mr Seibert said.
He said that it will consult with its partners in light of the Russian response “on an appropriate joint response”.
Mr Navalny’s allies in Russia have insisted he was deliberately poisoned by the country’s authorities, accusations that the Kremlin rejected as “empty noise”.
The Russian doctors who treated Mr Navalny in Siberia have repeatedly contested the German hospital’s conclusion, saying they had ruled out poisoning as a diagnosis and that their tests for poisonous substances came back negative.
Mr Navalny’s supporters believe that tea he drank before boarding his flight to Siberia was laced with poison – and that the Kremlin is behind both his illness and the delay in transferring him to a top German hospital.
He was flown to Berlin on a plane organised by supporters, which was equipped with advanced medical equipment, and was accompanied by German medical specialists.
When the plane arrived to collect him on Friday morning at his family’s behest, Mr Navalny’s doctors in Omsk initially said he was too unstable to move.
His supporters denounced that as a ploy by authorities to stall until any poison in his system would no longer be traceable.
The Omsk medical team relented only after a charity which had organised the medevac plane revealed that the German doctors had examined the politician and said he was fit to be transported.
The Kremlin denied that resistance to the transfer was political, with spokesman Dmitry Peskov saying it was purely a medical decision.