Khodorkovsky made his fortune from the privatization of Soviet state assets and the dominance of his oil company, Yukos. While he was in jail, Yukos was dismantled and sold off to its rivals. What was left of the company filed for bankruptcy in 2006.
Khodorkovsky released a brief statement which read, "On November 12, I asked the President of Russia to pardon me due to my family situation, and I am glad his decision was positive. The issue of admission of guilt was not raised."
(Read more: Why one oil tycoon expects a pardon from Putin)
Steven Eke, senior analyst on Russia and the Former Soviet Union at Control Risks, the global risk consultancy, told CNBC in a phone conversation that his "initial reaction is one of extreme surprise, given that as recently as July this year Putin was speaking about Khodorkovsky as somebody facing potentially new criminal charges in 2014."
Eke said that what can be inferred is that, during the time Khdorkovsky has been in prison, Putin has cemented his power and can be assured that his place in Russia is now unassailable.
"Putin no longer considers Khodorkovsky to represent any kind of personal or political threat," Eke said. "Certainly not a threat to the entrenched authoritarian political system that Putin oversees. I would also add that Putin probably believes the political system to be sufficiently stable and predictable to risk freeing Khodorkovsky given that he's given no indication that he will leave Russia."
John Lough, an associate fellow for the Russia and Eurasia program at the independent policy institute Chatham House, said that Khodorkovsky's release is not a turning point for Russia's politics or its economy, but that it was important to understand the calculations of Putin with regard to the international and domestic message it sends.
(Read more: More political drama ahead at the 2014 Olympics)
"In the run-up to the Sochi Olympics, he (Putin) is looking to portray himself in a different light," Lough said in a telephone interview. "He may have seen the events in Kiev in recent days and weeks as a reminder that you need to keep the more liberal and dynamic part of society in a state of slight suspense and keep them off balance, and you do that through a policy of sticks and carrots."
While Putin has stripped Khodorkovsky of the ability to run for office again and dismantling his company, Lough argued that Khodorkovsky could become a moral figurehead.