The militants were detained last year after authorities foiled the alleged IS-linked plot to shoot a rocket at an upmarket waterfront district of Singapore from the nearby Indonesian island of Batam. This charge was not proven in court.
Instead, the extremists were convicted of harbouring the Uighurs - members of a mostly Muslim Chinese minority who complain of persecution in their homeland of Xinjiang - on Batam and hiding information about them.
"The defendants have acted in an organised way and have deliberately aided terrorists," presiding judge Tarigan Muda Limbong told the West Jakarta district court.
The alleged plot to fire a rocket at Singapore's Marina Bay district was foiled in August last year. Authorities said the detained militants had hatched the plan with a leading Indonesian militant fighting with IS, who is accused of being behind a series of plots.
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It was not clear how advanced the plan was and analysts had expressed scepticism about the militants' capacity to carry it out.
It is unclear what happened to the second Uighur but he was believed to have been among several who entered Indonesia and tried to join an IS-linked group called Mujahideen of Eastern Indonesia on the central island of Sulawesi.
Indonesian militants fighting with IS in Syria are believed to have plotted with extremist networks back home to send Uighurs in Southeast Asia to Indonesia to join up with the Sulawesi group, which has almost been wiped out following a major offensive by security forces.
A crackdown had weakened the most dangerous networks but IS has proved a potent new rallying cry for radicals.
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