The European Offshore Wind Deployment Centre (EOWDC), which submitted the application, wants to build an 11-turbine test site off Aberdeen.
The council’s Formartine area voted nine against and one for the application.
The £230m (€270m) project received Scottish Government approval in March but it has long been opposed by US property investor, Donald Trump.
Trump is legally challenging the project off the Aberdeen coast, which is near his golf course in Balmadie, Aberdeenshire, in a four-day hearing that will take place from 12 November at the Court of Session.
Trump wrote on Twitter: "Great victory for people of Blackdog, Scotland. They defeated substation, stopping inefficient & ugly wind turbines."
He also wrote: "When will @AlexSalmond realize that he's destroying Scotland, the most beautiful countryside in the world w/ his stupid wind turbines?
"@AlexSalmond suffered a huge defeat by the people of Blackdog. Communities all over Scotland are fighting this loser.
Iain Todd, EOWDC's project spokesman, said: "We are extremely disappointed at the decision.
"We believe this a missed opportunity for the region and that we could have worked with Aberdeenshire Council to agree further conditions to progress the scheme.
"We will give careful consideration to the formal reasons for the decision before we decide our next steps."
This article was updated on 31 October 2013 to include the comments from the EOWDC consortium (from the eighth paragraph onwards).