The former oil tycoon was escorted out of his prison in northwestern Russia, in a hush-hush operation worked out behind the scenes with the German government and brokered by Berlin's former foreign minister Hans-Dietrich Genscher.
In a dizzying succession of events, the father of four then boarded a plane which the German foreign ministry later confirmed landed at Berlin's Schoenefeld airport.
A source told AFP that Khodorkovsky's ailing mother Marina, 79, was currently in Russia but planned to fly out on Saturday to Berlin where she has been undergoing treatment.
In his first remarks since his release, Khodorkovsky, once Russia's richest man, said his request for a pardon did not amount to an admission of guilt and thanked Genscher, German foreign minister from 1974-1992.
But in the statement released by his lawyers, he gave no clue about his future plans, saying only: "I am very much looking forward to the minute when I will be able to embrace my loved ones."
Khodorkovsky said he had made the pardon request to Putin on November 12 – even though his lawyers appeared to be completely unaware of the request when Putin announced the planned pardon on Thursday.
'Behind the scenes'
Putin stunned the country by saying his fierce critic had asked for clemency on humanitarian grounds as his mother was ill.
"Guided by humanitarian principles, I decree that Mikhail Borisovich Khodorkovsky... should be pardoned and freed from any further punishment in the form of imprisonment," said the Kremlin decree.
Less than three hours later, his lawyers said Khodorkovsky, 50, had left his prison colony in the town of Segezha in the Karelia region. The Russian prisons service said it had provided him with travel documents "at his own request".
Genscher, 86, arranged the flight on a private jet from Russia and picked Khodorkovsky up at the airport in Berlin. German Chancellor Angela Merkel's spokesman Steffen Seibert hailed the "behind the scenes" work of Genscher.
"He worked successfully on possibilities for a solution with a great level of commitment and the support of the chancellor and the foreign ministry," he said.
From the airport, Khodorkovsky was apparently taken to Berlin's luxury Adlon Hotel near the Brandenburg Gate from which Genscher was seen leaving in the early evening, national news agency DPA reported.
The release drew the curtain on the highest profile criminal case in post-Soviet Russia which has harmed the country's investment climate and become a symbol for the selective persecution of Kremlin foes under Putin.
"It has not sunk in yet," his mother Marina Khodorkovskaya told state television. Speaking in a shaky voice, she said she was taking sedatives to calm her nerves.
His father Boris told the Interfax news agency that they had only found out the news from the media. "We are attentively listening to the radio to follow all the news about our son," he said.
Meeting with secret services?
What role Khodorkovsky will play in Russia after his release is unclear, but it appears certain that Putin would never had allowed his freedom if he was seen as a threat. There is no indication of if or when he will return to Russia.
By accident or design, the release has coincided with a major amnesty for prisoners convicted of non-violent crimes that is expected to see the Pussy Riot punk rockers freed in the next days.
Thirty foreign and Russian Greenpeace activists, arrested on hooliganism charges after their protest against Arctic oil drilling, are also expected to escape prosecution.
Khodorkovsky had been due to be released in August 2014 but Russian prosecutors earlier this month raised the threat of a third trial for him on money-laundering charges.
Putin said on Thursday he saw no prospects for the third case.
The Kommersant broadsheet, citing sources, said Khodorkovsky had decided to seek a pardon after a recent meeting with representatives of Russia's security services.
Members of the security services told him the health of his mother, who has cancer, was worsening and warned him about a possible third case against him, the newspaper said.
Analysts put the release down to the Kremlin's bid to improve its dismal rights record and international image ahead of the Winter Olympic Games that Russia is hosting in February.
"In and of itself it will not change anything but it will give hope to investors," prominent economist Sergei Guriev, who co-authored a critical report on Khodorkovsky's second conviction in 2010, told AFP by email.
Supporters have said that Khodorkovsky had been thrown into jail and found guilty in two separate trials for daring to finance opposition to the Russian strongman.
He was snatched off his corporate plane in 2003 soon after Putin warned oligarchs against meddling in politics. He has been held in detention ever since.
He and his business partner Platon Lebedev were convicted of fraud and tax evasion in 2005. The pair were then convicted of embezzlement in a second trial in 2010. Lebedev's lawyers have said their client may also seek a pardon.