Jara was handed to a Red Cross delegation which also included Piedad Cordoba, a Colombian senator who had helped broker the handover.
Jara, 51, was abducted on by the Farc, or Revolutionary Armed Forces of Colombia, on June 15, 2001 while travelling on a main road in a United Nations vehicle in Colombia's Meta "department", or region.
Four hostages were also freed on Sunday in the first unilateral release of captives in almost a year, and the Farc have promised to release a sixth hostage, a provincial legislator, on Thursday.
Al Jazeera's Mariana Sanchez in Villavicencio says that with the release of Jara and the upcoming release of the legislator the Farc is giving up its last two civilian hostages - whom it considered its most valuable bargaining chips with the Colombian government - to send the message the group is adhering to international law and would like to be seen as open for dialogue with the government.
However, it remains to be seen what the Colombian government will do in response, she says.
The latest releases came amid complaints that the government had not halted all air force activity in the area for the hostage releases, as requested by the Farc.
The dispute caused a delay in Jara's release, which was first scheduled to take place on Monday.
The Colombian government issued a statement later on Monday vowing to suspend all air force activity in the affected areas during this week's planned hostage handovers.
The latest hostage releases also come two days after authorities blamed the Farc for a bomb explosion in the city of Cali on Sunday, which killed at least two people and wounded 39.
Farc has fought the Colombian government for decades in what it says is a continuing battle on behalf of the country's poor.
The group has been weakened considerably in recent years by a sustained Colombian military effort supported by $4bn from the US for sophisticated surveillance, communications intercepts and other tools.
It has also been weakened by the deaths of several senior commanders, desertions due to low morale and the rescue in July of a group of captives it had hoped to use as other bargaining chips, including Ingrid Betancourt, the French-Colombian politician, and three US contractors.