The game finally boiled over in the dying minutes when Stevenage had substitute striker Dino Maamria sent off for a violent incident.
Stevenage also had four players booked as they desperately tried to preserve their unbeaten home record.
But Grays showed far more craft and just about deserved to remain on top of the table and unbeaten away from home.
With the two defences not prepared to give an inch the midfield became almost like a minefield littered with fouls and skirmishes.
The game was less than five minutes old when Stevenage's Ollie Berquez and Grays' Stuart Thurgood were yellow carded after scuffling following a tackle.
Stevenage's Dannie Bulman then had to leave the field with a cut eyebrow but managed to return and complete the 90 minutes with his head swathed in bandages.
It was the hosts who came closest to scoring in the opening period when a close-range header from Anthony Elding was brilliantly tipped over the bar by Grays keeper Ashley Bayes.
But tempers continued to fray in the second half and within a minute Stevenage's Barry Laker was booked for a late tackle on Nathan Koo-Boothe.
Grays' Aaron McLean soon followed into the referee's book for a heavy tackle on Darryn Stamp but it was George Boyd, rumoured to be a £200,000 target for Leeds United, who almost broke the deadlock on 78 minutes when his rising shot from the edge of the penalty area beat Bayes but cannoned off the bar and out of play.
Grays' all-important goal came in controversial circumstances when they were awarded a penalty in the 81st minute after John Martin was brought down in the area.
Thurgood's spot-kick was brilliantly stopped by Stevenage keeper Alan Julian diving to his left, but the ball squirted from his grasp and Gary Hooper raced forward to whip the loose ball into the net.