The German Chancellor spoke to Mr Navalny at the hospital in Berlin where he is undergoing treatment for poisoning with the nerve agent Novichok.
Ms Merkel's spokesman confirmed the meeting took place but refused to give further details about how long it lasted and what was said. "It was a personal visit to Navalny in hospital," added Steffen Seibert.
Mr Navalny wrote on Twitter he was "very grateful to Chancellor Merkel for visiting me in hospital" but objected to reports in Germany suggesting it was a "secret". He added: "Rather, it was a private meeting and conversation with the family."
The prominent dissident politician fell ill during a flight from Siberia to Moscow on 20 August and spent two days in a coma before Russian officials allowed him to be flown to Berlin.
It was initially thought he was poisoned with a cup of tea he drank at Tomsk airport but his associates later said traces of novichok had been found on a bottle of water in his hotel room in the city.
Mr Navalny spent 32 days in the Charite hospital in Berlin before being discharged last week.
The poisoning was described as a "brutal, murderous attack" by vice-chancellor Olaf Scholz at a meeting of the VAP foreign press association in the German capital on Monday.
Mr Scholz said international organisations had independently confirmed that Navalny was poisoned with a nerve agent from the Novichok family. Experts found the substance was similar, albeit not identical, to the poison used against Sergei Skripal and his daughter in Salisbury in 2018.
"That is why we call on Russia to cooperate in the investigation," Mr Scholz added. "And of course, Europe will have to decide together on an appropriate response."
Russian authorities have denied any involvement in the poisoning and have even suggested that Mr Navlany coulld have taken it himself.
On Friday the Russian foreign ministry accused Germany of "megaphone diplomacy" and "a broad smear campaign baselessly accusing Russian authorities of allegedly poisoning the Russian citizen".
Since the suspected assassination attempt Ms Merkel has faced calls to halt the Nord Stream 2 pipeline, which is meant to bring more Russian gas directly to Germany.
However Mr Scholz said the project - a collaboration between Russia's state gas giant Gazprom and nearly 100 private companies including Shell and Uniper - would reduce Germany's dependence in the energy sector.
Additional reporting by agencies