In what was the Scots’ return to a major finals for the first time in 23 years, Patrik Schick headed the Czechs in front in their Euro 2020 opener three minutes before the interval.
The striker doubled that lead in the 52nd minute with a sensational effort from just over the halfway line which caught Marshall out of his goal and unable to get back.
After the game, Schick said he had planned his wonder goal in the first half after spotting Marshall, the penalty shoot-out hero for Scotland in the play-off final in Serbia, off his line, telling the BBC: “I knew he was staying very high and when the ball came I checked where he was standing.”
Clarke, who revealed Kieran Tierney has “a chance” of making Friday’s game against England having missed Monday’s opener through a niggle, said: “In the normal circumstances he is looking to sweep up behind his defence when it comes out.
“It is a fantastic finish.
“I think rather than looking to apportion blame all the time, sometimes you have to credit the goalscorer.
“The breaks went against us at the wrong time.
“Obviously losing a goal five minutes before half-time from a second phase of a set-play was disappointing for us.
“We normally defend that quite well.
“That was a blow. We came out second half and tried to get back in it. Jack (Hendry) hit the bar, and then had another shot that got blocked and fell straight to their striker and he produced a marvellous finish and from there it becomes a long, difficult afternoon.
“I thought we showed good invention, we had chances to get back into the game and if we could have made it 2-1 it could have been a different end to the afternoon.
“Disappointed but ready for the next one.”
Clarke admitted his preparations had to change with the injury to Arsenal defender Tierney.
He said: “We will work on him over the next few days and he has got a chance of being fit for Friday.
“Obviously we’d done a lot of work on team shape and Kieran was involved in that.
“With 48 hours to go when he picks up the little niggle that kept him out, it does take a little bit of changing, it changes the dynamic of the team.
“Kieran has been an integral part of how we have played recently but I don’t think we defended too badly.
“The moments in the game that got away from us; the first one is preventable, the second is really good.
“The dynamic was OK in the rest of the team. I went with Stuart Armstrong to get someone driving from midfield.
“The way the game panned out, there wasn’t much midfield play in the first half. It was only when the game opened up and when we started to get the opportunity to play through midfield that I thought we were decent and created some good chances.
“Sometimes a football match doesn’t go your way, today was that day.
“I don’t think there was much between the two sides if I am being honest.
“You look at our attempts at goal, our possession was good, we weren’t quite clinical enough.
“The game on Friday will take care of itself.”
Czech Republic coach Jaroslav Silhavy thought the start to the match was key to his side’s victory.
He said: “The decisive factor was that we survived the early pressure from Scotland.
“Then we got into the game and scored the opening goal.
“The second goal from Patrik calmed us down and finished the job.”