The court in the southeastern province's capital, Khorugh, sentenced Odil Ayombekov to 17 years and Hamza Murodov to 16 years in prison.
The two were convicted of murdering regional security chief General Abdullo Nazarov last summer.
The trial started February 19.
The defendants’ lawyers claimed Nazarov's death was unintentional manslaughter.
Tajik government forces conducted a military operation against the two defendants' armed supporters following Nazarov's killing.
Authorities say 13 security officers and 30 militants were killed in the operation, which lasted for several weeks.
However, local citizens say that at least 70 people lost their lives during the operation.