The restriction was in place because of the Australian Defence Force’s concerns about tall buildings in Darwin interfering with aircraft taking off from the nearby Air Force base.
Minister for Lands and Planning Dave Tollner announced buildings higher than 90 metres could now be considered for the CBD with the consent of the Department of Defence and civil aviation authorities.
"There are good reasons for allowing developers to consider building higher than the arbitrary 90-metre limit," he said in a statement.
"High-rise buildings are now a common feature of the CBD and this decision will help ease the demand for development elsewhere in Darwin.
"If we are to make the CBD a more vibrant place, encouraging more people to live and work there obviously makes sense."
Mr Tollner argued Darwin's 90-metre restrictions were higher than other cities.
"Most Australian capital cities have buildings over 200 metres, but Darwin's civilian and military aviation restrictions mean we're unlikely to see many buildings above half that height," he said in a statement.
The Chairman of the Northern Territory's Planning Commission Gary Nairn said there were no reasons for the restriction to remain in place.
"There were discussions with both defence and the civil aviation authority as to the reasoning why and the bottom line was that nobody could find an actual scientific reason why the 90-metre [restriction] existed," he told radio station Mix 1049 Darwin.
"They have basically said if somebody wants to do something higher than 90 metres then we'd like to have a look at it."
Mr Nairn also said there were several reasons for the amendment.
"I know when I first took on this role ... architects particularly were saying to me 'there are a number of restrictions within the planning scheme and it doesn't allow us to really be innovative'," he said.
"Height was one of them but the other one was the volumetric controls, and that's one of the other changes that the minister is announcing ... to provide the Development Consent Authority to have some flexibility in the way that they apply the volumetric controls."
The Northern Territory Government said applicants were required to seek consent from the Department of Defence, Darwin International Airport and the Federal Government's Department of Infrastructure and Regional Development for all buildings over 90 metres.
If these consents are obtained, potential developers will still need to seek approval through the NT's planning system for all other aspects of a development.
Former Lands and Planning Minister Peter Chandler exhibited the proposed amendment on September 15 2014 for 28 days, and a public hearing was held on November 21.
Thirteen submissions were made, including five objections.
The 55-metre height restriction on future development along the Esplanade and the 90-metre height restriction on future development along the south-western side of Mitchell Street will both be retained.
Darwin Waterfront precinct is outside the CBD and will not be affected by the amendment.