82-year-old, Thiruvendran Velupillai and his wife had been in military custody after their son was killed on May 18 in a battle with the army in northern Sri Lanka.
According to Army spokesman Brigadier Udaya Nanayakkara, Thiruvendran had been ailing for some time before he passed away.
Nanayakkara said he did not know the cause of death.
Prabhakaran's wife and three children also were killed by the military in the final phase of the military operation against the Liberation Tigers of Tamil Eelam (LTTE) rebel group.
The government declared victory on May 19 over the rebels after the deaths of Prabhakaran and the other top rebel leaders.