The hosts went ahead after just nine minutes when Pablo Mills and Micky Cummins linked through the middle for Cummins to feed Le Fondre just inside the area from where he made no mistake.
Le Fondre doubled the lead after 38 minutes, poking home a loose ball after Nick Colgan had saved a Cummins header from Nicky Law’s corner.
Between the goals, Grimsby’s Jean Louis Akpa-Akpro was denied by the legs of Andy Warrington but the second half was a drab affair.
Grimsby sent on substitute Adam Proudlock to improve their chances going forward, but it made little difference and Rotherham went off the boil until Le Fondre set up what looked an unmissable chance for Tom Pope but he shot wide with the goal at his mercy.
They grabbed a consolation in the second minute of added time when substitute Wes Fletcher went through unchallenged to shoot past Warrington.