The Scots had won their first five Group A qualifiers including a 2-0 win over the Spanish at Hampden Park in March, and they thought they had taken the lead when McTominay, who scored twice in Glasgow, fired in a wonderful free-kick in the 59th minute only to see it ruled out after a VAR check for a Jack Hendry infringement.
Alvaro Morata headed in after 73 minutes and substitute Oihan Sancet, making his debut, added a second in the 86th minute to leave Group A leaders Scotland three points ahead of Spain having played a game more.
Clarke’s men face France in a friendly in Lille next Tuesday but Spain face Norway in Oslo two days earlier and if the Norwegians drop points, Scotland’s place in Germany will be secured while the Scots also have Georgia away and Norway at home in November.
“The team played well and the players are disappointed,” said Clarke, who confirmed skipper Andy Robertson will go back to Liverpool for treatment with a shoulder injury which saw him replaced by Nathan Patterson just before the break.
“We came here determined to qualify. It hasn’t happened tonight but I think there was a lot to be pleased about in the performance.
“The big moment in the game is probably the close decision on the Scott McTominay goal.
“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 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.
“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.
“Tonight was a first chance to qualify. It has gone beyond us. Maybe the result on Sunday night goes in our favour and we qualify from that. But we won’t qualify from that, we will qualify for the work we have done, we have 15 points from six games.
“If the result doesn’t go our way and Norway then we have a very realistic chance in the two games in November to win the section.”
Spain boss Luis de la Fuente, speaking through an interpreter, was pleased with his side’s team spirit.
He said: “We knew they were a strong team and strong from set-pieces and free-kicks, and that free-kick, I was told it was offside and a foul on Unai Simon. We thought it was offside but in the end it was offside.
“Opponents always get chances we were prepared and very strong mentally.
“Even if the goal had stood I am convinced we would have reacted.
“It was a team effort and I value the hard work of the team because a game lasts 90 minutes and more.”
“Norway, will be different, a different team to Scotland. We will try to take initiative and cause them problems and minimise their offensive potential.”
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