The Scotland manager added that he has no fears about doing so again in the future if the teenager continues to struggle to break into the Everton first-team.
The full-back has found it hard to establish himself at Goodison Park since his move south from Rangers in January.
But he caught the eye again at right wing-back for Scotland in Thursday night’s 1-1 draw with Poland at Hampden Park.
Everton supporters took to social media in droves to question why Patterson was being kept out of the Everton first-team by Seamus Coleman and Jonjoe Kenny.
Patterson has played just 45 minutes for Everton. He was replaced at half-time of the FA Cup victory over Boreham Wood and hasn’t featured since under Frank Lampard.
But he was given 67 minutes against Poland as Scotland enjoyed a productive run-out in place of the postponed World Cup semi-final play-off clash with Ukraine. He could feature in the starting XI again on Tuesday when Scotland take on Austria in Vienna.
“I had no worries about Nathan, none whatsoever,” said Clarke. “I know the level he has gone down to train in and even just training at that level, working with English Premier League players, it’s a good level.
“As long as he’s doing his work properly on the training pitch then he’ll always have enough in his legs to come and play for us.
"I saw him stretching and when he starts to stretch you don’t want to risk an injury for the boy so we took him off. But his performance was really good for a boy who has had so little football.”
Patterson was an energetic presence on the right for Scotland and he proved their main attacking outlet in the first half with three shots. The first came via a mazy run where he beat three opponents. Everton fans were circulating clips of the solo effort on social media as they sought to understand why they had not seen more of the 19-year-old.
Clarke is simply glad he has Patterson and other young talents at his disposal. Billy Gilmour, 20, won his 11th cap in midfield while Aaron Hickey made his debut in the second half. The 19-year-old looked at home on the left during his 25 minutes on the pitch.
Clarke believes that having such youngsters at his or anyone else's disposal can only enhance Scotland's hopes of qualifying for the next four major finals.
“It’s good having these young players,” said Clarke. “Gilmour and Nathan Patterson played on Thursday, Aaron Hickey came off the bench.
“We have a good age so this group of players can go for another two, three or four tournaments if they want. That is fantastic for the future.
“Billy and Callum (McGregor) are two really good footballers on the ball,” he added. “We always try to play anyway, but when you have two players like that in midfield you have to give them the ball otherwise there’s no point in playing them.
“Even when we made the changes later in the game we didn’t dip too much, even though that would be normal if that happened.”