The Shots looked to be on their way to a first win in four games when Anthony Charles and Peter Vincenti scored early on but Le Fondre had other ideas.
The Shots were ahead as early as the fifth minute when unmarked centre-back Charles volleyed in Anthony Straker's cross.
Vincenti's tap in - after Danny Hylton capitalised on a poor Nick Fenton backpass - made it two six minutes later.
Rotherham finally stirred into life in the 25th minute when Liam Henderson went close, before Le Fondre slotted home from inside the area to reduce the arrears just after the half-hour.
And when Le Fondre's lobbed finish took him to 24 goals for the season 10 minutes after the restart, the Millers' comeback was complete.