The Alamedin district court in Bishkek also ruled that the property of Rustam Abdulin, Azamat Zakirov, and Yevgeny Golovin be confiscated.
Kyrgyzstan introduced a moratorium on executions in 1998.
Another 35 defendants, including ethnic Chechen criminal kingpin Aziz Batukaev, received extended jail terms of up to 22 years.
Akmatbaev was killed in a prison colony on October 20 while trying to mediate between security forces and rioting inmates.
His brother Rysbek, an alleged crime boss, was murdered on May 10 near Bishkek shortly after being elected to parliament.