The charity said the new technology would provide an alternative to road ambulance journeys, offering significantly quicker transport of vulnerable babies between hospitals.
The service began carrying Babypods for emergency missions in 2013.
But the new incubators will attach to existing equipment in the helicopter, providing warmth and oxygen.
They also have a transparent chamber, allowing babies to be monitored during flights.
Welsh medics went to Switzerland to help in the design process and, at a cost of Â£70,000 each, two new incubators have been bought by NHS Wales.
They will be used on Wales Air Ambulance's newest helicopter, the fourth in its fleet.
Weighing 15st 10lb (100kg), the incubators will be fitted to a sled and require two people to lift them into the air ambulance.
Since April 2015, helicopter crews have been joined on board by consultant doctors.
Dr Dindi Gill, the Emergency Medical Retrieval and Transfer Service Cymru interim director, said: "Having the incubator system will further enhance the ability of the EMRTS teams to manage neonates born at home or in hospital.
"It is recognised that temperature control is extremely important to this group of patients and, therefore, we welcome the ability to carry the incubator on Wales Air Ambulance's helicopters."
Following crew training, the incubator service will run as a trial to the end of 2016.

ITV's The Only Way is Essex (Towie) has been "largely positive" for Brentwood, where it is set, but "everything has a shelf-life", the council leader said.
Lisa Bone, of Visit Essex, added: "If its bubble bursts we could be left with stereotypes, not economic benefits".
A meeting is being held on Tuesday to discuss the town's "sustainability".
The show Towie, now in its 11th series, features ordinary people appearing in modified situations based on their actual lives.
Many run their own businesses in Brentwood, including shops, salons and nightclubs, which feature in the programme.
"Towie won't always be around and while it brings in a lot of tourism it has also given the town a certain stereotype, perception and image," Ms Bone said.
"Brentwood is full of beautiful historic buildings and family-friendly parks and we need to ensure we emphasise those, making the town attractive to everyone and ensuring its sustainability."
Borough council leader Louise McKinlay, said: "The popularity of the show has been very good for the town centre, retailers and the tourism trade, bringing so many people in to the area.
"Whether we like it or not, Towie has put Brentwood on the map. Yes, there's a lot about tans and nails in Towie, but there's also a great entrepreneurial spirit and that's evident everywhere in the town.
"I'd like to say that the only thing that's orange in Brentwood is our recycling bags."
Businesses in the town are being asked to consider Brentwood's "unique selling point and future branding" at Tuesday's meeting hosted by the council and Visit Essex.

The casualty, who was with a group of paragliders, was airlifted off Slieve Gullion at about 15:00 GMT on Sunday.
Mourne Mountain Rescue Team said the man had a "serious leg injury" and was taken to the Royal Victoria Hospital in Belfast.
The team had been training in the Annalong Valley when the emergency call came at 13:43 GMT.
Mourne Mountain Rescue Team, Belfast Coastguard, Irish coastguard, PSNI and the Northern Ireland Ambulance Service were all involved in the rescue.
"A total of 22 members responded and the team stood down at 18:17 GMT," Mourne Mountain Rescue said.
The most advanced flight incubators in the UK for sick babies will be used by Wales Air Ambulance later this month.
[NEXT_CONCEPT]
An Essex town buoyed by the popularity of a reality television show needs to plan for when the "bubble bursts", businesses have been told.
[NEXT_CONCEPT]
A paraglider has been rescued after being injured on a mountain in County Armagh.