Medy Elito set Dagenham on their way from the penalty spot and although Claude Davis equalised for Rotherham, Davis gave away the free-kick on the edge of the Rotherham penalty that brought the winner.
The set-piece was pulled back across the box and Luke Wilkinson fired home with eight minutes remaining.
Despite another disappointing home defeat, Evans said Rotherham were "outstanding from start to finish"
"We were disappointed at half time when it was still 0-0," he said. "Because our possession and attacking must have been over 90 per cent.
"We were disappointed with the penalty because it just looked as though the boy played for it, and we were disappointed with the second goal because one of our boys went to sleep and didn't do his job.
"Other than that, I thought my team was magnificent. It feels as though Dagenham have turned up with masks and sunglasses and gone away with the points.
"The linesman didn't give the penalty. He was instructed to give it by the referee and I don't want to say any more about the referee, but we have to deal with games like this and we are obviously disappointed.
"We had a load of chances. Dagenham could play Manchester United and never get battered like that, but you only get points and prizes if you get the ball in the net. They did it twice and we did it once."