McTominay thought that he had given Steve Clarke's side the lead in the Euro 2024 qualification match when his free kick from a narrow angle found the back of the net.
However, following a VAR check, the referee disallowed the goal for an offside, with Scotland defender Jack Hendry standing just in front of Spain goalkeeper Unai Simon.
There had been huge confusion over the decision, as it was initially suggested that Hendry had fouled Simon, before it was confirmed that offside was the reason for the disallowed goal.
Spain went on to score twice in the latter stages through Alvaro Morata and Oihan Sancet to record a 2-0 win, meaning that Scotland must wait to potentially secure qualification for Euro 2024.
La Roja will head to Norway on Sunday knowing that a victory would see them secure their position in next summer's European Championship.
Meanwhile, Scotland, who remain top of the section on 15 points from six matches, will qualify if third-placed Norway fail to overcome Spain.
De la Fuente also said after the clash with Scotland that he is expecting Norway to 'play better football' than La Roja's opponents on Thursday.
"It was offside - we thought it was a foul but in the end it was a disallowed goal so it does not matter either way," De la Fuente told reporters after the contest.
"We knew they (Scotland) were a strong team, especially at set pieces and free kicks. It was offside they tell me - we thought it was also a foul on Unai. Even if that goal had counted I am convinced we would be have reacted and won.
"Maybe today we played against the team who are best at set pieces in the group. It is very hard to mark them. They are very strong. They have specialists on these occasions.
"Fortunately we did not concede any goals and we need the same against Norway on Sunday. Norway are different to Scotland. They like to play a bit more which will suit us more."
Spain have now won four and lost one of their five matches in Group A, but they will be weakened against Norway, as both Nico Williams and Alejandro Balde have left the camp due to injuries.