MSP Fergus Ewing has refused planning consent for the 23-turbine Druim Ba wind farm in the Blairmore Estate, near Drumnadrochit, next to Loch Ness.
The minister said it would have “significant adverse” impacts on the landscape and residents living nearby.
Druim Ba Sustainable Energy Limited’s proposals were opposed by a public campaign and Highland Council.
In 2011, campaigners flew a blimp close to the proposed site to demonstrate the scale of the turbines.
The developer said the project would have supported 1,000 jobs over its lifetime and paid out £345,000-a-year to local community projects.
The turbines would have reached to 149.5m (490ft) from the ground to the tip of a blade at its highest point.
The windfarm would have been in a forestry plantation.
A Scottish Government spokesman said: “The Energy Minister concurred with the findings of the Public Inquiry Reporter that the number and height of the turbines would appear out of scale with the surrounding landscape and it would have significant adverse landscape and visual impacts.
“Mr Ewing was also concerned that the visual impact from nearby properties and the likely noise from the proposal would be detrimental to the residential amenities of several nearby properties.”
Dave Thompson, SNP MSP for Skye, Lochaber and Badenoch, has welcomed the news that consent has been refused.
He said: “This decision demonstrates that the local planning system in conjunction in this case with the Minister is working, and takes into account local objections before any development is given the go ahead.
“I remain in principle supportive of renewable energy, but only in cases where it is compatible with the planning system, and I am confident that our planning system will continue to perform this role in appraising all such developments.”
The original application submitted by Druim Ba Sustainable Energy Limited was for a 69MW, 23 turbine wind farm on Blairmore Estate, in the Highlands.
The Planning Authority, the Highland Council, objected to the application, stating that the developments conflicted with their planning policies and the size and massing of the proposed wind farm would have vast visual impact on properties and communities.
Mr Ewing said: “Scotland has enormous potential for renewable energy that is delivering jobs and investment across Scotland, and I am determined to ensure communities all over Scotland reap the benefit from renewable energy – but not at any cost and we will ensure a balanced approach in taking forward this policy, as we have in the past and will in future.
“The Scottish Government wants to see the right developments in the right places and Scottish planning policy is clear that the design and location of any wind farm should reflect the scale and character of the landscape and should be considered environmentally acceptable.”
The Scottish Government has determined 85 energy applications, including 58 renewable applications. Consent has been granted for 32 onshore wind, one offshore wind, 19 hydro, four wave and tidal; and 18 non-renewable projects since May 2007.
Consent has been refused for nine energy applications since May 2007 (including this refusal), all of which were onshore wind farms.