Health Secretary Nicola Sturgeon said the move was justified by the tough financial climate, and that the decision could save around 2 million across Scotland.
The Evening News revealed last month the Scottish Government was keen on curbing the rise in "distinction awards", which had reached 7 million last year in the area.
That figure sparked fury from hospital campaigners, who described the rates as "obscene".
But some feel bonuses are a good way to keep the best consultants in the NHS and dissuade them from pursuing private practice.
Today Ms Sturgeon said: "The health service, like the rest of the public sector, faces serious challenges.
"I recognise the significant cost of distinction awards and my decision to freeze the bonus scheme reflects the need to free up valuable resources that can be redirected to frontline healthcare."