Last January, the Swansea-born Shingler was named in Scotland coach Andy Robinson's initial RBS 6 Nations squad, but it quickly emerged that the London Irish player had been tied to Wales through his participation in an Under-20 match against France last year.
Although Murrayfield officials contested the Welsh claim on the player, their appeal was thrown out at an International Rugby Board council meeting in Dublin.
An IRB statement said: "Council, having considered all the facts and having heard submissions from the SRU and WRU legal representatives, dismissed the appeal and upheld the decision of the IRB regulations committee.
"The council therefore determined that Steven Shingler is tied to Wales in accordance with IRB regulation 8 and therefore is ineligible to represent another union."
Shingler may now pursue his case through the courts – almost certainly in Ireland – but that process is likely to be long-winded. Worse still, he is now effectively in international limbo, as there is little chance that Wales will actually select him in the foreseeable future.
Robinson expressed sympathy for Shingler's predicament. "The SRU have backed Steven Shingler totally and believed there was a case there," said the coach. "I really now feel for the player. This was an important choice for him to make it at a young age and it's unfortunate that we've lost the case.
"It's down to Steven now. I spoke to him last night and he needs to take this in. He has to take stock now of the decision that's been made and take clear advice."