The proposed Stronelairg wind farm will be developed by SSE Renewables on the Garrogie estate near Fort Augustus in the Highland Council area.
At the same time, an application to build the 21-turbine Newfield wind farm, with a maximum generating capacity of 63MW and located near Lockerbie in Dumfries and Galloway, has been refused on the grounds of unacceptable adverse visual, landscape and cumulative impacts.
Energy minister Fergus Ewing said the Stronelairg development will help "keep the lights on across our islands at a time where there is an increasingly tight gap between electricity supply and demand".
But conservationists are concerned about the impact it will have on Scotland's natural beauty.
Mr Ewing said: "The Stronelairg wind farm will create jobs both in its construction and during its lifetime.
"Once it is up and running, the wind farm will save thousands of tonnes of carbon dioxide each year and will be able to produce enough electricity to power thousands of homes in the Highlands.
"As well as bringing benefits to the local community, the Stronelairg wind farm will also benefit the wider Highland region through the provision of a sustainable development fund.
"Wind farms like Stronelairg play an important part in helping Scotland reach its target of the equivalent of 100% of electricity demand generated from renewables.
"We are already providing over a third of the UK's renewable electricity generation and helping to keep the lights on across our islands at a time where there is an increasingly tight gap between electricity supply and demand."
Helen McDade, head of policy for wild land conservationist the John Muir Trust, said: "This development flies in the face of advice from Scottish Natural Heritage, which objected to the development on the grounds that it would destroy the character of one of Scotland's key areas of wild land.
"SSE is a powerful multinational company with its HQ in Scotland and we know this project is worth many hundreds of millions to its shareholders.
"It is unfortunate that SSE's views seem to hold greater sway over ministers than the opinions of the Scottish Government's own expert body on the natural environment."
David Gibson, chief officer for the Mountaineering Council of Scotland, said said it will be "a massively intrusive industrial development".
He added: "The Scottish Government appears to be oblivious to the adverse impacts of such developments on tourism.
"Even research studies sponsored by the renewables industry itself already show a worrying and serious trend in the adverse impact on visitor intentions, based on their perceptions of wind farm developments."
Dave Thompson, SNP MSP for Skye, Lochaber and Badenoch, said: "This decision is fantastic news for the local area and the Highlands as a whole - and further confirmation of the potential for renewable energy not just to make our country greener - but also to create jobs and contribute to strengthening Scotland's economy."