The controversial plans were called in by the government after being rejected by Aberdeenshire Council last year.
In granting the application, finance secretary John Swinney said there was "a significant economic and social benefit".
The plans include construction of two golf courses, a 450-bedroom hotel and about 500 new homes.
Mr Swinney said: "I am content that there has been an efficient, transparent and inclusive process which has taken account of all of the relevant issues and the views expressed before, during and after the public inquiry.
"Having given careful consideration to the issues and arguments, I agree with the reporters' findings and reasoning, and with their recommendation that outline planning permission should be granted, subject to the satisfactory prior conclusion of necessary legal agreements.
"The reporters found there was significant economic and social benefit to be gained from this project, which has been a major consideration in my decision to grant outline planning permission."
Mr Trump today welcomed the decision.
He said: "We are greatly honoured by the positive decision and believe that the people of Scotland will be extremely happy with the final product.
"As I have often said, because of the quality of the land we are given to work with, we will build the greatest golf course in the world."