The changes on Friday followed a congress of the ruling Baath party earlier this month that moved to consolidate the Syrian President Bashar al-Assad's power base in the face of growing international pressure and domestic dissent.
General Fuad Nassif Kheirbek, a former chief of the military intelligence monitoring division, was chosen to head the domestic intelligence service, a Syrian official said.
He replaces moderate General Bahjat Suleiman, 57, who had been in the post for seven years - under both al-Assad and his late father Hafez al-Assad.
Al-Assad's brother-in-law, influential General Assef Shaukat was confirmed as head of military intelligence, the official said.
Shaukat has been serving in the role in an interim capacity since 14 February, the day the former Lebanese prime minister Rafiq al-Hariri was killed in an attack in Beirut which many in Lebanon blame on Damascus.
In the third appointment, General Hassan Khaluf was named deputy to General Ali Mamluk, who was named head of the intelligence service on Sunday.
During the four-day meeting earlier this month, several members of the ruling Baath party's old guard made way for figures close to the Syrian leader, and the national command was slimmed down from 21 to 14.