Nardiello poked home substitute Ben Pringle's left wing cross at the start of five minutes of added time after the visitors, who looked threatening most of the evening on the counter attack, had taken the lead through Matty Blair.
The Minstermen, who bagged their tenth away deadlock of the season, started the brighter and went close through Ashley Chambers.
At the other end Lee Frecklington missed the best chance of the first half for the Millers as his free kick whistled wide.
Jason Walker then rattled the bar with Andy Warrington providing a crucial touch to his powerful effort on the half hour.
Warrington was again called into action after the break as Blair found himself in the clear only for the stopper to make a fine save on his 200th league appearance for the club.
And after Johnny Mullins had gone inches within putting Rotherham ahead with a header from a corner, York, without a win in nine attempts, went ahead just after the hour as Blair rounded veteran Warrington and stuck the ball into the empty net.
But Nardiello had the final say as he fired in to give the home side a somewhat fortunate draw.