The agreement stresses the necessity of eliminating concerns over those doctrinal differences and agrees the formation of a committee of religious scholars to contain arguments and manage disputes.
It also calls for confronting the "American agenda" in Lebanon.
Ibrahim Amin al-Sayyed, head of Hezbollah's political council, represented Hezbollah in the signing ceremony, while the Salafists were represented by Sheikh Hassan al-Shahhal, who heads the BJM.
But another Salafist authority, Dai al-Islam al-Shahhal, one of the founders of the Salafist movement in the Lebanese city of Tripoli, criticised the deal.
"The Salafi movement totally rejects this document ... and [he] who signed it has no right to claim belonging to the Salafi movement or representing it," al-Shahhal said.
"This document is ... harmful to the Sunni community, and will end up in vain, God willing," he said.
Tripoli has been the scene of sectarian violence in recent months, with clashes between members of the rival Sunni Muslim and Alawite groups in the the neighbourhoods of Bab al-Tibbaneh and Jabal Mohsen claiming the lives of 23 people.
Last Thursday, a bomb attack near a bus stop in the city's busy commercial district, killed at least 18 people.