The defender rose to head in Jobi McAnuff's free-kick just after the hour mark to end Ipswich's three-match unbeaten run and maintain the Royals' play-off place.
The goal decided an eventful but at times scrappy encounter at the Madejski Stadium, during which both sides wasted a hatful of chances in front of goal.
Both Reading goalkeeper Adam Federici and Tractor Boys stopper Arran Lee-Barrett were on top form to deny their opponents on numerous occasions.
Federici saved well from Daryl Murphy and Jay Emmanuel-Thomas, who also hit the bar with a fizzing effort, while Lee-Barrett was on hand to prevent Adam Le Fondre and Simon Church from finding the net.
And in the end Pearce's impressive header was enough to give the hosts all three points.
Reading, who had netted three times in each of their last three home matches, started the match at a canter.
Pearce had a glorious chance to open the scoring for the Royals after eight minutes, but he could only direct his free header into the arms of Lee-Barrett.
Despite the home side's start, Ipswich came close to taking an early lead when Murphy wriggled free to get a shot on target.
The effort looked to be sliding into the net, but Federici got down to make a save.
The hosts retaliated quickly, and Le Fondre's claims for a penalty after the former Rotherham man went down under the presence of Ipswich centre-back Ibrahima Sonko were rejected by referee Jock Waugh.
In an end-to-end first quarter of the game, the Tractor Boys went close when a shot from Emmanuel-Thomas clipped the top of Federici's crossbar.
Michael Chopra tried his luck for the Suffolk outfit without success before Aaron Cresswell had Federici clambering across his goal as his 25-yard swerving attempt narrowly missed the target after 19 minutes.
Le Fondre was within a whisker of converting Jem Karacan's delightful cross nine minutes later, but the striker's outstretched leg could not connect with the ball with the goal gaping.
The match quietened down somewhat in the lead-up to half-time. Le Fondre saw his 35th-minute effort stopped by Lee-Barrett and Federici denied Emmanuel-Thomas at the other end as the teams went into the break goalless.
After the interval, Ipswich came closest to breaking the deadlock when Chopra bundled his shot wide from 10 yards from a tight angle as, despite the number of chances, the match looked destined to end up goalless.
In the end, however, it needed a defender to find the game's only goal.
Ipswich midfielder Lee Bowyer was penalised for handball, McAnuff's free-kick was met at the back post by Pearce and his powerful header beat Lee-Barrett and nestled in the back of the net after 64 minutes.
Church went close to doubling the Royals' advantage eight minutes later, but the Welshman's clever flick was kept out by Lee-Barrett.
Ipswich struggled to mount a recovery, as Reading enjoyed the better of the territory in the final stages.