The game had just entered stoppage time when Luke Rodgers ran onto a header by Lee Hughes and saw his shot cannon off the underside of the bar, bounce down and then come out.
It was a very close decision.
The assistant referee put his flag up, the ball had bounced just over the line and the Rotherham players in the vicinity did not argue.
Earlier, with an hour played, a raised flag from the other assistant was to deny Rotherham after Marcus Marshall fired home from 12 yards when Nicky Law's effort had been pushed out. Marshall's shot flew past a couple of players near the line, one of them Rotherham's Adam Le Fondre.
"The assistant referee said Alf (Le Fondre) got the last touch but he must have had good eyes to see that," said Rotherham manager Ronnie Moore.
"Alf says he didn't touch it. Had he done so, you can bet he would have stuck his arm up to claim it and gone off celebrating but he never reacted and so that might tell you something. We were very unfortunate.
"It was cruel to lose the way we did after playing so well following a difficult start and we more than matched them," added Moore. "If we show that sort of effort and determination for the rest of the season then we will get that third place."
In the first 15 minutes, Rodgers hit a post and Hughes headed against the bar.
Notts County: Schmeichel; Thompson, Edwards, Lee, Hunt; Westcarr (Hamshaw, 88), Ravenhill, Bishop, Davies; Rodgers (Hawley, 90), Hughes. Unused substitutes: Hoult, Canham, Fairclough, Clapham, Akinbiyi.
Rotherham United: Warrington; Lynch, Sharps, Mills, Gunning; Marshall, Harrison, Walker, Law; McAllister (Broughton, 65), Le Fondre. Unused substitutes: Annerson, Green, Fenton, Ellison, Bell-Baggie, Pope.
Referee: G Hegley (Cambs).
Man of the match: Marcus Marshall.
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