The shelter will be moved from the intersection of Highgate and Drivers Rd, in Maori Hill, and stored by the society.
It follows a public meeting held by the society last month in an attempt to save the shelter after the Dunedin City Council earmarked it for removal.
The shelter was built for passengers taking the tram from Maori Hill to Logan Park for the New Zealand and South Seas International Exhibition, held from 1925 to 1926.
The society wanted the council either to restore the bus stop or consider an alternative use for the structure.
Society chairman Andy Langford said the society was pleased with the DCC’s decision.
‘‘It is more positive than the alternative.’’
The society would now investigate several options, including sending it to Ferrymead in Christchurch to be part of the Dunedin trolley bus display there.
Mr Langford said a meeting would be held soon to discuss other options.
The shelter had not been used for two years after it was damaged by a vehicle, and since then only basic maintenance had been carried out to make the structure safe, the council said.
It decided to remove the shelter because its deteriorating corrugated iron roof was causing interference with a neighbouring cellphone tower.
A replacement bus stop has been located nearby at the top of Drivers Rd.
