Player-coach Yan Klukowski will now take charge on an interim basis, assisted by captain Jared Hodgkiss and the existing backroom staff.
In a short statement, Hereford manager Jon Hale thanked Gowling for his hard work and dedication during his time as manager and wished him well for the future.
The decision comes after Hereford lost 1-0 to Farsley Celtic yesterday, their third defeat on the spin.