A draw against La Roja would have been enough for Scotland to book their spot at Euro 2024, and they looked to have taken the lead on the hour courtesy of a thumping Scott McTominay free kick.
However, McTominay's effort was ruled out for an offside on Jack Hendry, who was standing just in front of Spain goalkeeper Unai Simon.
Clarke has said that there is "no way in the world" Simon would have kept out the effort regardless of Hendry's position, but the Scotland head coach refused to be too critical of the officials.
Alvaro Morata and Oihan Sancet went on to score for Spain in the latter stages, and a win for La Roja against Norway on Sunday would book their position in next summer's European Championship.
Meanwhile, if Norway fail to beat Spain, then Scotland's position would be secured, as the national side remain top of Group A, winning five of their six games in the section.
"At the time, we think it is a goal. You know when the referee gets told to look at it, he is probably going to chalk it off. They have made the call, there is no point in me going on about it," Clarke told reporters after the contest in Seville.
"I think there was a little bit of 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 no way in the world the keeper was saving that, no matter where Jack Hendry was.
"You just move on. It is a VAR decision that goes against you. When we conceded, it makes it more difficult and the second goal puts gloss on for Spain I don't think they deserve.
"We came here to show that we were a good team and I think tonight we showed that. Tonight was the first chance to qualify, maybe the result on Sunday night goes in our favour and we can qualify from that.
"But we don't qualify because of that result, we qualify because of the work we've done to have 15 points from six games.
"That's why we will qualify if a result goes our way over the weekend. If it doesn't go our way and Norway win, then we have a very realistic chance for the two games in November to win this section and that's what we'll focus on.
"We can be pleased with how we performed but the lads are really disappointed that we've lost the game because we didn't come here to lose."
Spain head coach Luis de la Fuente, meanwhile, insisted in his post-match press conference that his side would have won even if McTominay's goal had stood.