Shorey's quick free-kick, which pinged in off the post gave the Royals a dramatic first half lead.
Although Ade Akinbiyi went close to levelling the game in the second half, poor finishing and excellent goalkeeping from USA international Marcus Hahnemann kept the Potters out.
Stoke had gone four games without a win ahead of the visit of Reading yesterday, but Tony Pulis' squad had reason to be confident going into the fixture as their squad had been bolstered by the arrival of Michael Duberry.
But Wayne Thomas almost scuppered his team's assets only three minutes in when his short back pass was pounced upon by Dave Kitson, but the alert Ed de Goey reacted quick enough to prevent an opener.
The Phome side then took the offensive but struggled to find any clear route to goal with both Darel Russell and Ade Akinbiyi being pushed wide by the away side's clever back line.
Midwat through the first half both crossbars took a clattering in the space of three minutes. Firstly on 32, Clint Hill was spared after he misjudged a cross, sending the ball tantalisingly close to his own goal.
Shortly after, Lewis Neal supplied a swirling cross that was met by a flick-on from Gifton Noel-Williams but the towering forward could only watch as the ball bounced back off the crossbar.
Yet Reading opened the scoring four minutes before the break when Nicky Shorey caught the Stoke defence napping by taking his free-kick quickly.
The 20-yard left-footed shot swung sweetly into de Goey's top right-hand corner to the home crowd's disbelief.
Akinbiyi could have had a hat-trick of headers in the second half, but the lack of power and excellent goalkeeping by Marcus Hahnemann denied him even an equaliser.