The goals were a welcome relief for the home side after a scrappy first half when Brentford could have edged it.
Jo Kuffour gave Brentford early hopes of their first win in nine when he broke forward and produced a fierce shot from long range but the rising effort was well over Neil Cutler's bar.
But in a scrappy opening spell, Williamson curled in a testing cross after a short corner for Rotherham but Pablo Mills couldn't reach it with his head.
Dave Hibbert stooped to head a dangerous cross but he was beaten to it by giant centre-back Matt Heywood, before Williamson produced another chance with a 25 yarder that Stuart Nelson saved well.
Paul Brooker pounced when the ball broke kindly for him and snapped off a long-range effort that flew over Cutler's bar, before Rotherham's Ritchie Partridge had two chances in as many minutes, hoisting one over the bar and seeing Nelson save well again.
And when a free-kick came Rotherham's way, Williamson curled an intelligent dipping shot that almost crept under the bar but Nelson had it well covered.
Two minutes into the second half Rotherham went ahead with a stylish finish from midfielder Williamson.
Hoskins did superbly trying to force his way into the area and Adam Griffiths bundled him over for a free-kick and earned a booking.
Williamson sized up the 25-yard free-kick and curled it brilliantly into the top right-hand corner just out of reach of Nelson.
And 12 minutes later it was Williamson who hit Rotherham's second with an emphatic penalty after Will Hoskins was brought down by Adam Griffiths.
Delroy Facey came within a whisker of a third when his diving header hit the post in the dying seconds.