The £9 million development will see an extensive refurbishment of the National Sports Centre Inverclyde in Largs, North Ayrshire, Sport Secretary Shona Robison announced.
The para-sports hub - described as the first of its kind in the UK - will allow disabled athletes to train at "outstanding" fully integrated facilities in a wide range of sports.
It comes after Glasgow 2014 featured the highest number of para-sport medal events in the history of the Games, with Scottish athletes winning seven medals.
The Scottish Government will invest £6 million towards the refurbishment, which will also provide 60 fully adapted residential rooms.
The remaining £3 million will come from sportscotland, the national agency for sport.
Speaking ahead of a parliamentary debate on the legacy of Glasgow 2014 today, Ms Robison said: "Team Scotland para-athletes won an amazing seven medals, including three golds, at Glasgow 2014, inspiring more disabled people to take up and enjoy sport.
"This Government is focused on maximising the sporting legacy of the Games and this new funding for fully adapted accommodation will give a new generation of para-athletes the chance to train at world-class facilities and emulate their Games heroes.
"Inverclyde is already one of the best-equipped, modern residential sports centres in the UK and is integral to the Scottish sport system that is producing Commonwealth and world champions.
"The redevelopment will help even more para-athletes train in outstanding facilities, with the best technical support, to become world beaters.
"That is another positive and lasting legacy from the Games for Scottish sport."
The Largs-based centre already includes an international standard gymnastics training facility, an indoor 3G pitch, two squash courts and a dance studio.
Outdoor facilities include four full-sized grass football pitches, a synthetic hockey pitch, four synthetic tennis courts, a golf development course and a target range.
The redevelopment is to be completed in 2016 and it is hoped the facility will also benefit young people who want to participate in a range of para-sports.
Stewart Harris, sportscotland's chief executive, said: "Scotland has world-class sporting facilities and this significant commitment, coupled with the National Performance Centre for Sport being built in Edinburgh, further improves Scotland's sporting infrastructure.
"The integration of para-sports into the Glasgow Games was hugely successful and this announcement builds on that by offering local, regional, and national clubs and schools capacity to ensure special needs groups and children with disabilities, as well as performance para-athletes, benefit from using world-class facilities."
Gavin McLeod, chief executive of Scottish Disability Sport (SDS), said he was "delighted" the investment would see the centre become fully inclusive.
He added: "SDS is committed to supporting children, young people and adults with a disability to participate and compete in their chosen sport and meet their full potential. This investment will undoubtedly support SDS to achieve this aim."
Speaking at Holyrood, Ms Robison said: "Our para-athletes have performed fabulously at these games, winning seven para-sports medals.
"That is why I am delighted to announce today £6 million investment for a new national para-sports centre.
"Based in Largs, Scotland's national centre will nurture and hone future sporting talent here in Scotland.
"It will complement our network of world-class facilities and will allow for a future Erraid Davies, who amazed us at Tollcross, and Neil Fachie and Aileen McGlynn, who rode us to the podium in the velodrome.
"This centre will be the first of its kind in the UK and a testament that sport can be a powerful catalyst for change."
Labour sports spokeswoman Patricia Ferguson said: "I am delighted with the announcement that the Cabinet Secretary has made today about the facility, as she knows I have had a keen interest in disability sport for a long time now.
"I think it is entirely fitting that we take this step building on what happened at the Commonwealth Games and recognising that while para-sports has always been integrated into the Commonwealth Games, it has not been integrated quite to the extent it has been on this occasion."
Conservative sports spokeswoman Liz Smith said: "In the context of Largs, we have to change the public perception, culture and attitude to ensure participation and development.
"The Games obviously revealed some inspirational examples that can facilitate the shift in that perspective.
"The extraordinary achievement of England's Steve Way, who in 2007 weighed 16 and half stone and smoked 20 a day, but in Glasgow 2014 he finished 10th in the marathon, breaking the British over-40s record which had stood since 1979.
"Or who could forget the delightful Erraid Davies, the 13-year-old Shetland swimmer who won bronze the 100m para-breast stroke. It showed just how much could be done with even modest means.
"She trains in a pool that is about a third of the length of the one in which she won her medal and she has proved what can be done without necessarily world-class facilities in which to train."