The increase for GPs is in line with a deal for other NHS staff in the country from April.
Health Secretary Alex Neil said: "Yesterday, I confirmed that the Scottish Government will ensure that our hard-working and dedicated NHS staff rightly receive the wage increases they were promised.
"I am pleased that today we are able to offer the same pay increase for GPs.
"In fact, the £6 million investment in primary care goes beyond the recommendations of the review body on doctors and dentists' pay because we recognise the valuable role that GPs and their staff play in providing health care services at the heart of our communities to improve the public's health."
The extra money takes the total funding for primary care services to £14 million since 2013, the Government said.
Mr Neil announced yesterday that nurses will get a 1% pay rise, giving them a better deal than their counterparts in England.
The increase includes extra money for staff earning under £21,000 to ensure their pay goes up by £300.
The changes follow recommendations from NHS pay review body and Doctors and Dentists Pay Review Body.