The midfielder's strike was controversially ruled out in Scotland's 2-0 defeat by Spain on Thursday.
It looked like Steve Clarke's side had taken the lead in the Euro 2024 qualifier in Seville when the Manchester United star fired in a free-kick from almost on the byline just before the hour mark.
However, after a VAR intervention, Dutch referee Serdar Gozubuyuk was sent to check his pitchside monitor and he initially signalled for a Jack Hendry foul on goalkeeper Unai Simon.
UEFA told STV Sport on Friday, however, the goal was ruled out for offside against the former Dundee and Celtic defender.
Alvaro Morata headed in after 73 minutes and substitute Oihan Sancet added a second in the 86th minute to leave Clarke's men three points ahead of Spain at the top of Group A having played a game more.
Afterwards a disappointed Clarke was keen to move on but the PA news agency understands the SFA has contacted UEFA referees' committee chairman Rosetti looking for an explanation on the process of the decision and the confusion and the conflicting information.
The SFA also expressed a frustration at some refereeing inconsistencies, such as the apparently clear foul on Scotland midfielder John McGinn by Dani Carvajal at the edge of the Spain penalty area in the first half being ignored.
Also, no action was taken when a Spain player had his arms wrapped around Scotland striker Lyndon Dykes when McTominay fired his free-kick into the net.
It was a first defeat in six Group A qualifiers after five wins but Scotland are still in a strong position to qualify for Germany, three points ahead of Spain at the top of the section having played a game more.
Spain face third-placed Norway in Oslo on Sunday and if the Norwegians drop points, Scotland's place in the finals in Germany will be secured.
The Scots also have Georgia away and Norway at home in November.
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