Nakheel had previously sought to make Ahmed Al Muhairi pay an extra Dh3.1 million (US$844,000) for two villas after denying the former board member of its parent company, Dubai World, a 15 per cent "staff discount" available on the developer's properties.
Mr Al Muhairi sued Nakheel to obtain the 15 per cent discount and won the case.
Sir John Chadwick, the Tribunal judge, said there was no basis behind Nakheel's assertion that Mr Al Muhairi was not an employee of Dubai World when he entered into a contract to purchase the properties.
"[Mr Al Muhairi] says he was an employee of Dubai World, Dubai World says he was an employee of Dubai World," said Sir John.
Mr Al Muhairi has held several senior positions in Dubai, including director at Istithmar World, part of Dubai World, and a board member of the mortgage provider Tamweel.
He is the chairman of the Ports, Customs and Free Zone Corporation, in addition to his Dubai Customs role.
"This was a significant decision and the client is extremely pleased. It further illustrates to Dubai and the world that the Dubai World Tribunal is a valuable asset to the region's dispute resolution process," said Joe Durkin, a partner at Davidson & Co, the law firm representing Mr Al Muhairi. Nakheel declined to comment on the ruling.
The developer had originally granted Mr Al Muhairi a discount on the properties after he had presented a letter from the human resources department at Dubai World, confirming he was an employee.
Nakheel had agreed to offer the discount when Mr Al Muhairi purchased the properties, and part of the contract was drafted to that effect.
But more than nine months after the deal was signed, the management of Nakheel had not given Mr Al Muhairi the title deeds to the properties and said he was not eligible for a discount, offering no reason for the rebuttal.
Chris O'Donnell, the previous chief executive of Nakheel, wrote to Mr Al Muhairi on February 9 last year saying "your request has been reviewed by the Nakheel management and we regretfully inform you that the decision is that the staff discount cannot be applied to the aforesaid properties", court documents showed.
Mr Al Muhairi then sought a court injunction to allow him to obtain the 15 per cent staff discount on the two villas on the Palm Jumeirah - number 119 on frond B and number 143 on frond D.
He was also awarded Dh175,000 in court costs.