The IRB council ruled unanimously that Shingler was "captured" by Wales after playing in an Under-20 international against France in 2011.
The eligibility row was sparked when 20-year-old Shingler, a Swansea-born fly-half or centre, was included in Scotland's RBS 6 Nations squad earlier this year, believing he qualified through his Dumfries-born mother.
The Scottish Rugby Union appealed against the original decision that Shingler was tied to Wales, made by the IRB's regulations committee, but the former Scarlets back now faces a future devoid of Test rugby - unless there is a reconciliation with Wales.
Scotland head coach Andy Robinson was "disappointed" with the ruling.
Robinson told Press Association Sport: "I really feel for the player, because he made what was probably a difficult decision at the time to choose to play for Scotland.
"He believed he was qualified to do that and put all his eggs in that basket and it's been taken away from him. That's disappointing."
Asked whether the SRU and Shingler will take the case further, Robinson said: "That will be for Steven to now consider what he wants to do."
Although Shingler had represented Wales Under-20s, the SRU argued he had never signed a declaration tying his international eligibility to Wales.
The SRU cited the complex cases of Matthew Jarvis and James Loxton, who played for Wales Under-20s in 2010 before switching their allegiance to Ireland.
The cases of Jarvis and Loxton prompted a global review, which recommended playing for an Under-20 team should no longer commit that player to that nation.
But that recommendation was dismissed by the IRB, who determined the Under-20s can be considered as the next senior national team.
The IRB instructed unions to publicly publish their second team designation on an annual basis and ensure that all players are informed.
The Welsh Rugby Union welcomed the verdict.
WRU head of rugby Joe Lydon said: "It was vitally important that the WRU defended its stance over this issue. It was certainly not just about the individual player concerned but a case of needing total clarity on the situation, both retrospectively and going forward."
Shingler's brother Aaron made his Wales Test debut at flanker against Scotland in the Six Nations in February and has been selected for the summer fixture with the Barbarians and the Tour to Australia.
For his younger brother, who was behind Rhys Priestland and Dan Biggar, among others, in the Wales reckoning, an international career now appears an unlikely prospect.
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