Town lost their grip on three points in the closing stages for a second successive weekend to go down to their fifth consecutive Championship defeat.
Josh Carson's deflected effort off the leg of Kaspars Gorkss looked to have proved the difference for Town after the Latvia international had himself levelled matters at the other end just minutes earlier.
But, just a week after Ipswich conceded twice late on at Nottingham Forest to go down 3-2, Pearce headed the visitors level in the 90th minute and then Hunt piled on the misery in injury time.
Fit-again Daryl Murphy, on loan from Celtic, had earlier marked his return after a two-month absence due to a hamstring injury with a second-half header from skipper Grant Leadbitter's well-taken free-kick.
With the scoreline just 1-0 with 75 minutes on the clock, the late drama proved the highlight of an otherwise low-key encounter played out amid a subdued atmosphere at Portman Road.
Ipswich boss Paul Jewell made four changes to his XI, including a first appearance since New Year's Day - and a first for Town in two years - for goalkeeper Richard Wright after he re-signed for the club for a third spell earlier this week.
Left-back Ian Harte and striker Simon Church came in for Reading.
And it was Church who came within a whisker of scoring what would have been only Reading's second first-half goal of the season after just two minutes but he failed to poke home Jimmy Kebe's teasing cross.
The visitors were unable to capitalise on a total of six corners within the opening quarter, two of which would have presented clear openings should a Reading shirt have been able to connect with the inswinging deliveries.
Hunt nodded Shaun Cummings' cross wide when he really should have done better.
However, the closest chance of the first half did fall Ipswich's way after 34 minutes as Keith Andrews put Michael Chopra through and his shot rolled past goalkeeper Adam Federici before rebounding off a post, with the striker's attempted rebound well blocked.
The second half continued in much the same fashion as the first.
Federici did well to stand up to Andrews' fierce free-kick after 54 minutes, but the Reading stopper was beaten soon after.
Leadbitter sent over a great free-kick from the left and Murphy headed into the bottom corner from the centre of the penalty area.
Brain McDermott sent on Adam Le Fondre and Hal Robson-Kanu in a bid to salvage a point and it was Hunt who almost did just only to see his cross tipped over by Wright.
An equaliser finally did arrive in the 76th minute as Gorkss headed home Harte's right-wing free-kick.
But the visitors' jubilation lasted just three minutes before Carson's innocuous effort looped over the helpless Federici.
However, it was Reading who enjoyed the last laugh as they salvaged a memorable victory thanks to Pearce's header and Hunt's low finish late on.