Pogrebnyak broke the deadlock following a Stephen Bywater howler just before half-time and centre-back Pearce volleyed home Reading's second in the 72nd minute.
Williams then added a third four minutes later with Reading having now scored 15 goals in their last four games while Millwall crashed to their sixth league defeat in nine.
Millwall started brightly and on three minutes Reading goalkeeper Alex McCarthy flung up a left hand to keep out Lions striker DJ Campbell's snapshot from 10 yards.
Three minutes later Pogrebnyak released Jobi McAnuff on the left but his low cross-shot eluded Adam Le Fondre and drifted wide of the post.
An end-to-end start then saw McCarthy claim a floated Ryan Fredericks cross before Lions keeper Bywater comfortably caught a bobbling Williams strike.
In the 11th minute Pearce could only head a Millwall corner partially clear and Steve Morison volleyed the resulting rebound just over the bar.
Williams lofted the ball over the top for Pogrebnyak to chase after 15 minutes but, having reached the penalty area, the big Russian striker's progress was stopped by Mark Beevers.
Bywater palmed Jordan Obita's low free-kick behind after 17 minutes following a foul on McAnuff by Spurs loanee midfielder Fredericks.
And after Garath McCleary had got in behind Scott Malone a minute later, Danny Shittu made a vital block to concede another corner.
After 25 minutes Pearce's long defensive header caught out the Millwall backline but Bywater was quickly off his to clear ahead of Pogrebnyak.
Three minutes later McCleary weaved his way past three Millwall defenders on the left and then found Le Fondre who lashed his shot well off target.
The Royals went in front after 39 minutes when Bywater dropped Chris Gunter's high ball into the box and Pogrebnyak latched onto it, shifted the ball onto his left foot and smashed home.
On the stroke of half-time the Royals could have doubled their lead but Le Fondre was unable to reach McAnuff's fizzed cross.
Six minutes after the break former Norwich striker Morison put Liam Feeney through on goal but McCarthy was able to hold onto his angled drive.
Lions midfielder Josh Wright was only able to shoot tamely at McCarthy after 56 minutes having chested the ball down on the edge of the box.
In the 72nd minute Pearce volleyed home to double Reading's advantage after Bywater had done well to tip Pogrebnyak's close-range header away.
And soon after Williams made the points safe by breaking through the Millwall backline before slotting into the far corner.