The red-hot striker netted after 61 minutes when Marcus Marshall’s cross caused havoc, Nick Fenton mis-kicked, Craig McAllister’s shot was saved by Tony Roberts, only for Le Fondre to slam home the rebound.
Defeat was harsh on Daggers as they had the better of the chances, especially in the second half.
Josh Scott had gone closest in the opening 45 minutes but glanced his header wide of the target, while after the break, Paul Benson’s effort was just over the bar.
Rotherham threatened briefly before they scored, with Josh Walker’s drive saved by Roberts, and they defended stoutly once Le Fondre broke the deadlock.
Substitute Phil Walsh should have secured a point for the home side but headed Danny Green’s pinpoint cross over, and then failed to convert another opportunity after the winger beat both Kevin Ellison and Mark Lynch with some dazzling skill.