Spokesman Richard Broome says eight other drivers who had been suspended Sept. 30 were reinstated after they agreed to time their prayers.
Broome says clocking out is a reasonable requirement because some employees had failed to return to work promptly after prayers. The drivers move rental cars for cleaning and refueling.
Teamsters Local 117 has filed an unfair labor practices complaint with the National Labor Relations Board. The union also is filing religious discrimination charges with the EEOC.
The union represents nearly 80 Hertz drivers who earn between $9.15 and $9.95 an hour. About 70 percent are Muslims.
