Steve Clarke's side were left outraged after the Manchester United star's free-kick was ruled out, a decision that proved key in the outcome of the match.
With the score 0-0, McTominay scored a glorious free-kick from near the byline, however the effort was ruled out by VAR.
This was due to Jack Hendry being offside and 'interfering' with play in front of Spanish goalkeeper Unai Simon.
The decision not only halted Scotland's elated celebrations, but turned them to fury, with McTominay seen throwing a water bottle at the ground.
However an alternate, behind-the-goal camera angle seemingly confirmed that Hendry's presence had little bearing on the goal.
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It was Spain who ended up coming away with a 2-0 win thanks to an Alvaro Morata effort and a Ryan Porteous own goal.
Scotland manager Steve Clarke said: "They have made the call, there is no point me going on about it.
"I think there was a little bit confusion at the time, whether it was offside or for a foul on the keeper.
"If you take those two together, Jack Hendry was marginally offside and when he steps towards the goalkeeper they have interpreted that as Jack being involved in the play but I will tell you now there is now way in the world the keeper was saving that no matter where Jack Hendry was.
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"You just move on, it is a VAR decision that goes against you."
A victory would have wrapped up qualification for Euro 2024, however Scotland still remain in a strong position at the top of Group A with 15 points.
Spain are now second with 12 points with Scotland set to qualify if Spain beat third-place Norway on Sunday.
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