The MoD said recovery teams had found the remains of Flt Lt Adam Sanders, 27, who grew up in Lancashire, and Sqd Ldr Samuel Bailey, from Nottingham.
They were two of the three RAF crew members who died when the incident happened during a training flight in the north of Scotland on 3 July.
The sole survivor of the crash is still in hospital.
The funeral of Flt Lt Hywel Poole, 28, who died in hospital after being airlifted from the scene, was held in Wales on Wednesday afternoon.
The RAF confirmed it has now completed the recovery of wreckage from the crash site.
But the search for other debris, which may have been carried away by the tide, will continue along the coastline, involving coastguard and the RAF Mountain Rescue team.
The RAF said in a statement: “The next of kin of the aircrew involved in this tragic incident, and all at RAF Lossiemouth, are very grateful for the tremendous show of public support that has been evident.”
The Military Aviation Authority added: “The recovery of wreckage has now been completed and the Service Inquiry Panel, assisted by the Military Air Accident Investigation Branch, will continue to work quickly and thoroughly to investigate the circumstances of the accident.”
The planes from 15 (Reserve) Sqd at RAF Lossiemouth crashed into the sea south of Wick, Caithness.