Intense pressure from local MPs and influential groups had failed to move the MoD to act.
However, the junior defence minister, Lord Howe, announced low flying would be cut after a review of the distribution of training across Britain.
The inquiry discovered that the Borders area had received more than a "reasonable share" of low flying by jets at heights between 250ft and 100ft.
Lord Howe said: "I am pleased to say that steps have been taken to spread operational low flying more evenly across the available areas.
"This will result in less being carried out in the Borders, which is certainly good news for people in that area, who we know find this type of low flying a particular irritant."
In future, low flying will be spread more evenly over the available areas in Britain.
Sir David Steel, Liberal Democrat MP for Tweeddale, Ettrick and Lauderdale, said: "Every week my mail bag receives complaints about low flying and this announcement will be welcomed in the Borders."
However, what is good news for the Borders is bad news for the northern Highlands, which will see more low flying.
The MoD explained that the population density in that region was lower than in the Borders and stressed that it hoped the annoyance would be kept to a minimum.