Johnny Mullins, Jamie Annerson and Paul Warne (all knee) remain absent.
But the Millers were stunned when Clovis Kamdjo (36) opened the scoring for the visitors, heading in from Mark Marshall’s corner.
Rotherham equalised at the start of the second half, good work from Danny Schofield saw Troy Brown level.
Yet it was short-lived, as Izale McLeod pounced from the penalty spot to make it 2-1 to Barnet on 63 minutes.
Rotherham’s Mark Bradley hit the bar before Le Fondre levelled when he raced on to Danny Harrison’s pass and shot into the net through Dean Brill’s legs.
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