West Ham boss Pardew was making his first return since an acrimonious and long drawn-out departure from Reading in September.
The Royals eventually received more than £300,000 compensation after chairman John Madejski had forced Pardew to take a period of gardening leave before taking over as Hammers boss.
But the three points secured by Kitson would have been far sweeter payback for the Reading fans who booed Pardew from the moment he arrived at the ground right through to the final whistle.
Pardew has invested heavily in West Ham since taking over, but Steve Coppell, his replacement at Reading and former manager at Crystal Palace, has done his own rebuilding job with the Royals.
And it was Kitson, one of several Coppell new boys, who put the home side in front ten minutes before half time.
Kitson and Dean Morgan, another Coppell signing, were preferred up front to Shaun Goater and Lloyd Owusu and would have represented something of an unknown quantity to Pardew.
Defender Andy Melville was clearly in the dark too, as he allowed Graeme Murty's searching ball into the box to run behind him, where Kitson anticipated the flight to sidefoot cleverly past goalkeeper Stephen Bywater.
Kitson was a constant danger to the West Ham defence and was denied an early opening when Bywater punched clear a Paul Brooker cross from right under the striker's nose.
But West Ham had enjoyed the better of the first-half openings before the home side's crucial breakthrough.
Marlon Harewood, sacrificed in a tactical switch by Pardew after less than half an hour, was on long enough to see a stinging shot brilliantly palmed away by young Reading keeper Jamie Ashdown, who was given his senior break by Pardew two seasons ago.
Then David Connolly, a striker Pardew attempted to sign for Reading last summer, stole in between the home side's central defenders and poked inches wide of Ashdown's left-hand post.
The lively Morgan saw a shot flash just wide after outpacing Melville before Kitson made the breakthrough for Reading, but West Ham had penalty appeals waved away just before the interval when Michael Carrick tumbled under a sliding challenge from James Harper.
West Ham came out full of fire at the start of the second half but their added bite was blunted by a second Kitson strike eight minutes into the second half.
Tomas Repka was booked for pushing Steve Sidwell off the ball and the outstanding Harper's floated free-kick fell kindly for Kitson, who lashed a fierce left-foot half-volley into the roof of Bywater's net.
Reading's makeshift defence, with midfielders Andy Hughes and Ricky Newman plugging gaps left by injury, were rarely troubled after that as West Ham gave up the fight all too easily, though it took a last-ditch tackle from Ivar Ingimarsson to deny substitute Don Hutchison in the final minute.
By then, the delirious home fans were taunting their former manager with cries of "Pardew out" and the Hammers boss admitted he had endured a miserable return.
MAN OF THE MATCH: Dave Kitson (Reading) - Scored both the goals with clinical finishes but was a handful for the West Ham defenders throughout.