Lyon conceded 215 runs in the second innings of the eight-wicket loss but Clarke believes that the spinner's confidence has not been dented by the display in Chennai.
Australia's captain told reporters: "On grounds in India it's very easy to go for a lot more runs because they're smaller and have fast outfields. I thought Lyno showed his character in the second innings.
"I wish we had 150-200 runs on the board because then he would have had the opportunity to bowl in inconsistent spin, pace and bounce on a day-five wicket that I know he would have loved. He's been fine [since the Test]. He's working hard every day to try and get better."
The second Test match starts in Hyderabad on Saturday.