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.
The most advanced flight incubators in the UK for sick babies will be used by Wales Air Ambulance later this month.