It was Rotherham who should have taken the lead before half time. First Alan Lee missed a sitter and then new boy on-loan Gareth Farrelly blasted another effort against the post on his.
But Paul Warne scored his first goal in Division One this season after 12 minutes as Rotherham made the most of a mistake by Hessenthaler - the Gills player-manager failing to clear the ball and Farrelly's cross was knocked in by Warne.
However Hessenthaler played a part in the equaliser, when his corner was flicked on at the near post by Mark Saunders and Rod Wallace headed in from an acute angle from the far post to put Gillingham back on terms.
Lee will have nightmares about his miss. He seemed to have done the difficult part dragging the ball around Jason Brown on the edge of the area but, with an open goal at his mercy, fired wide.
Rotherham centre half Guy Branston was sent off eight minutes from time for a second bookable offence.
Rotherham boss Ronnie Moore said: "I think we should have won the game bearing in mind the chances we had but Alan Lee missed a sitter which must go down as one of the misses of the season."
Hessenthaler said: "It was an awful game to play in and it must have been awful for the fans as well.
"It was the worst we're played on our problem pitch, but it's another point and it means that we've reached fifty which was my first aim at the start of the season."