Daggers had chances to take an early lead but Jon Nurse and Paul Benson failed to hit the target.
And those misses proved costly as Ronnie Moore, who rang the changes at the Don Valley Stadium, saw his side break the deadlock after just 11 minutes. Kevin Ellison mis-hit a shot and Le Fondre was in the right place at the right time to turn the ball into the net from close range.
Rotherham could have moved further in front but Dagenham goalkeeper Tony Roberts produced a string of fine saves to keep out Gary Roberts and Le Fondre.
But the Millers doubled their advantage from the spot after 34 minutes when Mark Arber fouled Le Fondre in the box and the striker picked himself up to score his 21st goal of the season.
Andy Warrington had to be alert to deny Nurse in the second half, while Le Fondre could have had a hat-trick if his curling effort had not gone just the wrong side of an upright.