Virtually everyone in the ground saw the ball go over the line by at least a foot except the officials.
The game began scrappily with both sides content to play long balls into each others centre-backs with the few moments of inspiration coming from Gillingham's debutant Tommy Black.
The Millers' best spell came midway through the first half. The Gills defence struggled to clear Will Hoskins' cross and Stephen Quinn had a shot charged down by Sean Clohessy.
Jason Brown was called into action moments later when he tipped over John Mullin's shot from the edge of the penalty area.
At half-time Gillingham boss Ronnie Jepson brought on Gavin Grant and Michael Flynn for the ineffective duo of Neil Harris and Alan Pouton in a bid to pep up the home side's game but instead it was the away team who took the lead after 55 minutes.
Jepson's gamble eventually did pay off when Grant bagged the equaliser and his first ever goal for the club. Black's corner was swung into the near post and Grant stooped to head home.
The home side continued to press for the decisive second and nearly got it when Black's shot from 20 yards was deflected narrowly wide.
With five minutes to go Baker thought he had given Rotherham the points when his header hit the post and appeared to cross the line but Mr Hill's decision left the Millers incensed.