Le Fondre hooked home a Liam Henderson cross in the 89th minute to give the Millers the lead for the first time with his 21st goal of the season.
And Taylor finished off a breakaway attack by the visitors in the fifth minute of added time to get the Millers promotion push back on track.
Burton made a flying start when the recalled Greg Pearson headed them in front after only 51 seconds, but their joy was short-lived as the Millers replied with a headed equaliser in the fifth minute from Johnny Mullins.
Paul Peschisolido’s men regained the lead in the 34th minute when midfielder Aaron Webster linked well with Russell Penn before steering a 12-yard shot past Warrington.
Webster squandered the chance to double Burton’s lead in the 49th minute when he slammed a spot kick against the crossbar after Maghoma had been tripped by Marcus Marshall.
Rotherham made the most of the escape to claw their way back to level terms in the 75th minute when Marcus Marshall headed home before Le Fondre and Taylor sealed victory.