Clarke, who retired after last year's Ashes defeat in England, expressed his surprise at the decision on Twitter on Wednesday.
"I would of (sic) liked to have seen the captain play until the series was won and then have a rest," Clarke said.
"In the same breath, if Smithy needed a break then he should have flown home after the Test matches not 2x ODIs in."
His sentiments were echoed by former opener Michael Slater but Lehmann said he had no issue with the comments.
"We respect our former captains and former greats having an opinion," he said.
"There is no dramas about it and they're entitled to it. But we think it's the best for Steven to get him right and ready to go.
"It's hard captaining in all three formats and we are just making sure he gets a break."