Kitson missed a sitter in the first half at Fratton Park on Tuesday night but made amends shortly after the break with a well-taken volley from Liam Lawrence's corner.
Both sides hit the woodwork during a first half dominated by Pompey and Kitson's strike was no more than Steve Cotterill's team deserved.
Jamie Ashdown kept his side ahead with a superb point-blank save to thwart Noel Hunt as Reading, unlike against Leicester on Saturday, looked lightweight in attack without last season's top goalscorer Shane Long.
Portsmouth made two changes following the home defeat to Brighton at the weekend. Jason Pearce and Kitson came into the side at the expense of Joel Ward and Hermann Hreidarsson.
Benjani Mwaruwari started on the bench on his return to Fratton Park.
Reading were unchanged from the team that started the impressive 2-0 win at Leicester.
Greg Halford hit the crossbar early on against his old club with a shot from just outside the box.
But it was another former Royal who should have opened the scoring soon afterwards when Kitson was put through on goal by Hayden Mullins only to shoot tamely at Adam Federici.
Jimmy Kebe's diving header from Jobi McAnuff's cross looked like going in the top corner but struck the woodwork just after the half-hour.
Back at the other end, David Norris steered a shot wide from close range after he was set up by Luke Varney and Nwankwo Kanu stung Federici's palms with a 25-yard shot.
Pompey continued to put Reading under pressure and made the breakthrough after 51 minutes when the unmarked Kitson volleyed home from 10 yards out.
Federici tipped another long-range effort from Kanu over the crossbar before his opposite number Ashdown reacted quickly to deny Hunt midway through the second half.
Benjani was given a rousing reception on his return to Fratton Park, where he hit a hat-trick in a 3-1 win against Derby on his last appearance for Pompey on January 19, 2008.
He replaced Kanu and soon set up Varney with a beautifully-weighted pass with the outside of his foot which the former Blackpool striker volleyed just wide.
Reading applied some late pressure but last season's Championship play-off finalists could not fashion an opening.
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