Storchak, 54, who oversaw foreign debt talks at the ministry and was a key figure in Russia's talks with the Paris Club, was detained last November and accused of attempting to embezzle $43 million from the state. He was released from Lefortovo pre-trial detention center in Moscow.
He was greeted with applause from journalists and flowers from supporters.
Sporting long wavy hair and a big, bushy beard, Storchak said that he had kept up with news from the financial markets while he was in custody.
He said he did not know why he had been released from custody, but thanked the investigation team for the "unexpected" decision.
Investigators from the Prosecutor General's office said that they had taken the decision to release Storchak and a second suspect, Viktor Zakharov, general director of the company Sodexim, as the investigation was over and they were unable to influence it.
Russian prosecutors filed final charges against Storchak earlier this month. In addition to the embezzlement charges, Storchak was also charged with abuse of office.
Storchak has maintained his innocence throughout the investigation. If convicted, he faces between five and 10 years in prison.
The former finance official said he was grateful for the support from his wife and children as well as from Finance Minister Alexei Kudrin and the staff of the Finance Ministry.
Earlier in the day, Kudrin welcomed the investigators' decision to release Storchak.
"It was originally my proposal to release [Storchak] with a pledge not to leave the country. I believe the accusations are unfair and unfounded," Kudrin said. "I believe that all of us will be convinced of that and I believe that justice has prevailed."
Some analysts see the case against Storchak as a sign of a power struggle within the Kremlin between free-market liberals such as Kudrin and conservative elements favoring a greater role for the state in the economy.