Former US Open champion McDowell, 37, has fallen to number 83 in the world and was not one of Clarke's three wildcard selections for Hazeltine.
"G-Mac is a good friend and I was speaking to him frequently during the qualifying process," said Clarke, 48.
"It was very difficult, but he is just not firing on all cylinders right now."
McDowell has played in the last four Ryder Cups - holing the winning putt in 2010 at Celtic Manor - and Clarke said it would be strange not having his compatriot around Europe's Ryder Cup team later this month.
But he has been impressed by the reaction of the Portrush-raised player to his disappointment of missing out on the team for the first time in a decade.
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"The messages he has sent show the class of the man," said Clarke.
"He has been wishing us all the best and volunteering to help in any way he can."
The European captain also says he is not worried that six of his team have not played in the Ryder Cup before.
Danny Willett, Thomas Pieters, Rafael Cabrera-Bello, Andy Sullivan, Matt Fitzpatrick and Chris Wood will make their debuts in Minnesota from 30 September to 2 October.
"The Ryder Cup will be different to anything they have played in before, but they aren't rookies anymore really," added the former Open champion.
"They play all over the world and I have confidence that the guys will go over there and perform.
"The Americans are desperate to win the cup back but I believe in our team."
European Ryder Cup captain Darren Clarke admits it was difficult to leave his close friend Graeme McDowell out of the team to face the United States.