Mayoral Committee Member for Safety and Security, JP Smith, says the decision follows a lengthy revision of the race event plans and supporting documents required by the Events By-Law.
He says the City is satisfied that the event organiser has met all requirements.
Churches have expressed concern that the race will impact on congregants wanting to worship during Easter.
Smith says there is now a clear traffic plan for churches that will ensure that services can go ahead.
He says traffic services will work with marathon marshals to ensure worshippers are able to gain access to intersections along the route.