All the goals came in the final half-hour as the Royals capitalised on a Hammers implosion, with both Joey O'Brien and Jack Collison seeing red.
Centre-back Pearce beat visiting keeper Robert Green from eight yards out midway through the second period, following good work from Jobi McAnuff, to hand the hosts the lead.
West Ham, who have now lost back-to-back Championship matches after their home defeat to Burnley last weekend, could not generate any momentum over the course of the 90 minutes and were not helped by the dismissal of O'Brien moments before Reading's first strike.
O'Brien received the first red card of his career for a second, needless yellow card after a trip on McAnuff and the Hammers struggled to contain their hosts without him.
Once Pearce had slotted home it was all one-way traffic at the Madejski Stadium, and substitute Church tapped home Adam Le Fondre's chip to seal the victory for the Royals before Collison was dismissed for a wild challenge on Jimmy Kebe late on.
Not satisfied with one goal after coming off the bench, Church nodded home Ian Harte's set-piece with four minutes left to round off the scoring.
Reading had the first significant chance of the game after just seven minutes. Le Fondre fizzed the ball across the face of the goal and Noel Hunt, back in the starting line-up after a head injury, narrowly failed to connect as he slid in.
West Ham's best opportunity of the first half-hour came when Collison blazed over from inside the area, while at the other end Jimmy Kebe had a good chance to open the scoring.
The Mali winger, although a long way from goal, had the net at his mercy when Green missed opposite number Adam Federici's long free-kick. However, Kebe could not control his effort on the half-volley and shot wide.
Jem Karacan also failed to hit the target with a curling effort from distance as neither side were able to work the goalkeepers over the course of the first 30 minutes.
The visitors were struggling to reach their fluent best, but almost claimed the advantage in the moments before the break. Collison's corner was headed across goal and Papa Bouba Diop thought he had poked home, only for Hunt to get in the way on the line and clear.
Almost straight away the Royals rallied, and Karacan was within centimetres of finding the net with his flying header from Kebe's whipped centre.
The scrappy nature of the contest continued into the second period and West Ham took almost 20 minutes of the half to have their first shot on target before the match then exploded into life.
O'Brien foolishly tripped McAnuff to earn his second yellow card of the afternoon and moments after he left the field, Reading went a goal up.
From the free-kick given for O'Brien's offence, Harte's delivery was not cleared properly, McAnuff slipped the ball into Pearce's path and the centre-back side-footed home from eight yards out.
In an instant the home side were dominant and went two up when Church was on hand to tap home Le Fondre's chipped centre from close range.
West Ham lost all their shape and discipline, and soon found themselves reduced to nine men when Collison needlessly raked his studs down Kebe's legs.
From the resulting free-kick Church headed home Harte's cross to intensify the misery for the Hammers.