In a lively but quite even affair, Rodgers blasted home a left foot shot via the underside of the bar past Andy Warrington after a long punt downfield from Casper Schmeichel was headed on by Lee Hughes.
It was Notts who started much the brighter, with Craig Westcarr hitting the post from a Rodgers centre and then Hughes himself having a goal ruled out for offside and hitting the top of the bar.
After a whirlwind 20 minutes though the game settled a touch and the Millers found their feet.
Adam Le Fondre had their best effort of the half shortly afterwards as he made space for himself but shot wide from 20 yards as the game failed to live upto it's early billing, with both teams cautiously cancelling eachother out.
In a role reversal, Rotherham were the better side after the break, and thought they'd taken the lead on 54 minutes but Marcus Marshall's effort after Schmeichel had parried Nicky Law's shot across the box became the second strike of the afternoon ruled out for offside.
It appeared however that Le Fondre, flagged as being in an active position, didn't get a touch to the ball on it's way in.
In the final 20 minutes County had their better spell of the second 45, as Hughes saw a header cleared off the line by Ian Sharps but in truth a point would have been a fairer result.
But with just a few moments left Rodgers struck the cruel blow as the Millers slipped out of the top three.
The afternoon was marred by the hostile goings on directed towards Hughes from the stands which involved a Millers fan entering the field of play at the final whistle.