The union said it has been persuading the department to withdraw a rule that introduced new working hours.
"As a result, workers were forced to work under these unbearable working hours, as consequences workers were subjected to disciplinary hearings while others were given leave without pay for not complying with the circular," the union said on Friday.
"The signed agreement confirms the withdrawal of the circular and that workers will revert back to the working conditions that were applied prior to the introduction of the imposed new working hours by the department's director general."
The dispute saw employees threatening to down tools and demanding overtime payment for working on Saturdays. Nehawu has argued that Saturday work should not be compulsory but voluntary for the employees.
The department would not budge and said there was no overtime for employees. The union said it proposed that the new agreement be tabled at the bargaining chamber. The home affairs department processes passports for travel as well as registration of birth, marriage and death certificates.