Instead, both sides preserved their unbeaten start to the season but Rotherham had the better late chances to claim the points.
After a dismal goalless first half Rotherham went ahead when striker Chris O'Grady notched up his second goal of the season when he crashed in a fierce left foot shot after 56 minutes after springing the offside trap.
Chester, managed by former Millmoor goal ace Bobby Williamson, should have been level soon afterwards but defender Ian Sharps blocked a goalbound shot from John Murphy with his knee after Andy Warrington had pulled off a point blank save, injuring his shoulder in the process.
But the Blues finally grabbed the equaliser they deserved after 72 minutes when 17 year old Kevin Roberts, who was on as a second half sub, grabbed his first career goal.
The youngster, currently being tracked by Bolton and Spurs, powered a header that beat keeper Andy Warrnington but hit the post and rebounded kindly, allowing Roberts to head into the open goal.
Rotherham provided all the late drama and had the chances to claim the winner even before the last gasp penalty appeal. But Chester keeper John Danby was in defiant form pulling off a string of impressive late stops.
The best of the chances fell to O'Grady, Harrison and Stephen Brogan who all produced shots that could have seen Rotherham overtake Chester but for the efforts of the agile Danby, who also tipped over a Coughlan header at the death.
Mark Robins said of the controversy: "It was a definite penalty and we are very disappointed. For me from where I was there was no doubt and the lads all thought it was a penalty.
"He has put his arms up towards the ball. The referee said the incident was ball to hand but how can that be when he was moving his hands across your face and above his head?
"I'm really disappointed that we didn't take the three points but I think we looked sluggish throughout the game."
Chester manager Bobby Williamson diplomatically claimed: "Kevin Ellison told me the ball hit him in the face but I'll reserve my judgement until I've seen the video, players sometimes tell you things and make you into a liar.
"But I think we worked hard and deserved a point. This is a difficult venue to come to and Rotherham will win more here than they lose so we have to be happy with a point."