Roman Bogdanyants covered his face as he was escorted by police from the building, followed by a Russian man that police spokesman Francisco Ruiz identified as a former hostage.
While hostage negotiators were talking with the suspect, police surrounded the four-story building, which is located near several other embassies, including that of Venezuela.
The standoff, which lasted more than three hours, began when Bogdanyans, a Kazakhstan native who arrived in Costa Rica in 2005, seized part of the building Friday, holding Russian Ambassador Valery Nikolayenko and seven others hostage.
Officials originally reported an armed gunman had seized eight hostages, quickly releasing five. But Russian Ambassador Valery Nikolayenko told Channel 7 Telenoticias in a phone interview during the standoff that he and three other officials had remained in the building to help negotiate a peaceful end to the conflict.
Costa Rican media gave conflicting reports about why the suspect took the hostages. Some said he was angry that a visa request had been rejected, while others claimed his family had been a victim of fraud.
A family friend, Artur Mitiniani, told Channel 7 that the family had lost $54,000 because of problems with a Russian citizen who Bogdanyants met at the embassy.
In July 2004, a Costa Rican security guard took several hostages at the Chilean Embassy where he worked in San Jose, eventually killing himself and three embassy employees. The guard, Orlando Jimenez, 54, was upset about a pending transfer.