The Scots face Switzerland, who defeated Hungary 3-1 on Saturday, in Cologne before finishing their group campaign against the Hungarians on 23 June in Stuttgart.
Clarke insisted Scotland can still qualify for the knockout stages but admitted they will need a minimum of four points and have lost the “little safety net” of a higher goal difference when it comes to potentially finishing as one of the best third-place sides.
“We believe in ourselves – there’s no danger of that,” Clarke said. “We know it was a bad night.
“We have to accept all the criticism that comes our way and then we have to put it right. To be in football, you have to be very resilient.”
Ryan Porteous’ first-half red card for a dangerous tackle on Germany midfielder Ilkay Gundogan compounded Scotland’s struggles in Munich.
Clarke backed the Watford centre-half, who will miss the Switzerland game through suspension, amid criticism of his challenge.
“He hasn’t been sent off for a couple of years, Ryan,” Clarke pointed out. “He’s been great for us since I gave him his chance in Ukraine.
“The other night he was trying to stop a clear goalscoring opportunity. He definitely went in too hard and we’re all pleased that Gundogan has no lasting damage.
“It is something Ryan will learn, but it was an honest challenge to try to get the ball. I wouldn’t be too hard on him.”