The Millers registered their first point under new boss Neil Redfearn as they rallied in the second half and cancelled out Nick Blackman's stunning opener when Danny Collins converted from a corner.
It was a spirited display from Redfearn's men in the second 45 minutes and it ended the Royals' four-game winning streak.
And the former Liverpool and Chelsea coach admitted his side were troubled in South Yorkshire.
"I thought we had decent control in the first half and the second goal in the game was going to be crucial and obviously it went to Rotherham and at the end I was probably happy to take the point back down the road," he said.
"Credit to Rotherham I thought they were
excellent tonight, especially in the second half.
“They made a proper game of it in the
second half, that is the first time I have seen my back four stretched like
that this season, so credit to Rotherham.”
Reading's display was a far cry from the side that arrived at New York in April, where Clarke was left to talk about "a squad in decay" after a 2-1 loss, which secured the Millers' survival.
The Royals have made big strides in the few months since that game and are looking like genuine promotion contenders as the book-ended the 1-1 draw with dominant spells.
And Clarke knows how much they have improved since the last trip to New York.
"At the end of last season when I came here I was
quite scathing of my team and what I thought of the group, I felt there was
something that needed to change," he said. "It has been a really busy summer for us, we
changed a lot behind the scenes, we changed a lot of personnel.
"The owners gave
me a lot of backing in the summer to go out and be creative in the transfer
market. We haven’t spent a lot of money.
"We can be pleased with the progress we
have made in a short pace of time. To be near the top of the league is where we
want to be."
