Jalili succeeds former nuclear chief and current parliament speaker Ali Larijani as Khamenei's representative.
"You are expected to be able to help the power and independence of the Islamic system by active participation and constant exchange of views with me," Khamenei said in a letter to Jalili carried by the state broadcaster.
Jalili, who is a close ally of President Mahmoud Ahmadinejad, replaced Larijani as the head of the national security council after he stepped down over differences with Ahmadinejad.
In a separate decree, Khamenei, who has the final say in all key policy issues, appointed former parliament speaker Gholam Ali Hadad Adel as his own top advisor.