Ryan Christie put the visitors ahead in the 33rd minute of the Nations League game, Igor Matanovic levelling three minutes later.
Andrej Kramaric headed the home side in front after 70 minutes, but in the fifth minute of added time Scotland had the ball in the net with substitute Che Adams in the thick of the action, only for VAR to chalk the effort off for offside.
The Scots have lost all three of their games in the competition ahead of the visit of Portugal on Tuesday night and have only one win in 15 games as Clarke deals with an injury-hit squad.
However, the Scotland boss remains optimistic.
He said: “The disappointment is massive. You get that high at the end when you think you have a deserved draw and that is taken away by VAR.
“The performance was really good. I thought we were brave with the ball. We tried to play, tried to create chances.
“On another night we would’ve got what we deserved.
“A full squad fit and healthy would be a help.
“I briefly spoke to the players because there’s so much disappointment in the dressing room that it’s probably better to wait until we get back to Glasgow before we get a proper chat about the game, but just to believe we are on the right path.
At some stage we'll get a rub of the green, we'll get a bounce of the ball, we'll get a break and things will change
Steve Clarke
“We haven’t regressed as I said yesterday. We just have to keep believing, keep pushing away.
“This is what we have to do. Like I said before, they have to keep believing that we’re on the right path.
“We certainly send them that message. They must feel themselves coming off the pitch that they were very competitive against a good side.
“So we’ll try to take that into Tuesday night. At some stage we’ll get a rub of the green, we’ll get a bounce of the ball, we’ll get a break and things will change.”
Clarke was pleased with 18-year-old attacker Ben Doak’s first start but cautioned against too much hype for the Liverpool youngster, who is on loan at Middlesbrough.
He said: “I’m really pleased for Ben and as a coach I’m pleased with Ben. That’s his first start, I’m sure it won’t be his last.
“He’s got attributes and qualities. That’s why he’s in the squad.
“That’s why I tried to put him in the squad in the summer before his injury showed up. We see what Ben’s got for us. But we’re also careful.
“You have to be careful with young players. You have to bring them through at the right time.
“Obviously, injury-wise, it’s probably accelerated his debut. And his debut was good or his first start was good.
“We can build on that. Whether he’s got the legs and the energy to go on Tuesday night after such a big shift tonight, we can assess over the next couple of days. Let’s enjoy Ben, but let’s not put too much pressure on him.
“He’s got a great attitude. Very open. Determined to improve and stuff like that. He knows that he’s got parts he’s given and he has to improve. He’s not a shy boy. He’s a good character.”
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