They said he had driven Noordin to meetings with terrorists, booked a room in West Java where the hotel attacks were planned and transported explosive materials to a house where a truck bomb was being assembled for an attack on Yudhoyono's presidential convoy.
The truck bomb was intended for an attack around Indonesia's independence day on August 17 last year, but it never took place.
Amir, 35, was the third person to be sentenced for the July 17, 2009, bomb attacks at the Ritz-Carlton and JW Marriott hotels.
The same court had previously jailed Saefudin Zuhri, an in-law of Noordin, and Aris Susanto, who was sentenced to eight years for assisting and harbouring Noordin and two other suspects.
Nordin was killed with the other suspects in raids by anti-terror squads in September, two months after the hotel bombings.
Prosecutors had sought 10 years' jail for Amir, who indicated after the court sentencing that he would not appeal the decision.
"I don't understand the law but I accept the verdict," Amir told reporters.
Judges said they had imposed a lighter sentence than sought by prosecutors because Amir had cooperated with police and shown regret.
Indonesia has battled groups with links to al-Qaeda since 2002, when a bomb attack on a nightclub district on the island of Bali killed 202 people, most of them foreigners.
Since then, a regional security crackdown has seen hundreds of suspected JI members killed or captured and convicted.