The separatists had convicted Tudor Petrov-Popa of terrorism. The last of four prisoners held by Trans-Dniester since a 1992 civil war with Moldova, he was driven to the border with Moldova and released by the Trans-Dniester militia.
The four had been members of the Popular Moldovan Front, a party which backed independence for Moldova in 1991. Trans-Dniester, which is not recognized internationally, is inhabited by Russian speakers, with many Russian military families living in the region.
Petrov-Popa, 44, was greeted by dozens of supporters, including former fellow prisoner Alexandru Lesco, freed in 2004 after serving a 12-year term. Lesco draped a national flag on Petrov-Popa's shoulders in an emotional encounter.
On Saturday, the separatists freed another member of the group, Andrei Ivantoc. The former leader of the Popular Moldovan Front, Ilie Ilascu, was released in 2001 and moved to Romania, where he became a lawmaker.
The four have called for the reunification of Moldova with Romania, from which it was annexed in 1945 by the Soviet Union.
Russia maintains about 1,500 troops in Trans-Dniester despite requests by Moldova and the West to honor commitments to pull them out.
In 2005, the European Court for Human Rights ordered the separatists, Moldova and Russia to free Ivantoc and Petrov-Popa. The court also ordered Moldova and Russia - which backs Trans-Dniester - to pay the four a total of EUR750,000 (US$1,000,000) in compensation for the deprivation of their freedom, and for torture and inhumane treatment while in custody.
Some in Moldova and neighboring Romania saw the group's members as martyrs for their opposition to the separatists.