“Navalny's condition is stable,” said Jaka Bizilj, the head of the Cinema for Peace NGO after the flight touched down at Berlin's Tegel airport.
The air ambulance landed at 8:47 am local time (0647 GMT) at the military wing of Tegel airport after a day-long standoff over his medical evacuation.
His spokeswoman Kira Yarmysh confirmed the landing, tweeting that “the plane with Alexei just landed in Berlin”.
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Ambulances seen at the airport were expected to transfer him to Berlin's Charite hospital for treatment.
The 44-year-old lawyer and anti-corruption campaigner, one of President Vladimir Putin's fiercest critics, went into a coma after falling suddenly ill on Thursday on a plane to Moscow that had to make an emergency landing in Omsk.
Aides say they believe Navalny was poisoned, apparently by a cup of tea at the airport, and blamed Putin, though Russian doctors said tests showed no trace of any poison.
Doctors treating him in Omsk had refused to let Navalny leave but reversed course after his family and staff demanded he be allowed to travel to Germany.
As the plane left Omsk at around 8:00 am local time (0200 GMT), Navalny's wife Yulia posted a picture on Instagram of him being carried on a covered stretcher and thanked supporters for their “persistence”.
“Without your support, we wouldn't have been able to take him!” she wrote.
The ambulance arrived at the Omsk Emergency Hospital No. 1 early Saturday and masked medics put Navalny inside on a stretcher.
Russian doctors have said he is in a coma and breathing through a ventilator in a grave state.
They have said tests did not find any trace of poison, however, that Navalny appeared to have a “metabolic disorder” and to have suffered a sharp drop in blood sugar levels.
The regional interior ministry said police detected an industrial chemical after swabbing Navalny and his luggage, although doctors said this would not have caused his condition.
The air ambulance arrived in Omsk on Friday morning but Russian doctors initially said Navalny was too “unstable” to be moved.
Appeal to Putin
They announced on Friday evening they had agreed to let him be transferred after German doctors examined him and the Cinema for Peace foundation said they were “willing and able” to transport him to Berlin.
The turnaround also followed a letter from Navalny's wife with a direct appeal to Putin and after aides asked the European Court of Human Rights to intervene with the Russian government.
Navalny is the latest in a long line of Kremlin critics who have fallen seriously ill or died in apparent poisonings.
His wife told journalists that she wanted Navalny to be “in an independent hospital, whose doctors we trust”.
Many supporters expressed relief he was going for treatment outside Russia.
“I feel as relieved now as if terrorists had freed a hostage after long negotiations,” fellow opposition politician Ilya Yashin tweeted, criticising the delay in Navalny's departure. “I want to believe that this wasted time won't cost Alexei his life.”