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The Royals had looked set to take a 1-0 advantage into Wednesday's second leg at the Madejski Stadium when Nicky Forster gave them a 25th minute lead with his 17th goal of the season.
But Wolves turned the game on its head with two goals in the last 15 minutes and to add to Reading's misery, substitute Nathan Tyson was sent off for an injury-time lunge on Wolves' central defender Paul Butler.
Before Forster silenced the partisan crowd, Wolves had created chances of their own, starting after just four minutes when Denis Irwin lifted his free-kick over the bar.
Despite not creating much the Royals dominated much of the game and will certainly feel hard done by to come away with a defeat. Pardew's side certainly had the bit between their teeth, surging forward deep into Wolves territory straight from kick off.
Colin Cameron had a snap shot saved by Hahnemann, while skipper Paul Ince and leading scorer Kenny Miller both flashed efforts wide.
Reading proved to be more clinical when they created their one real opening of the first period.
Left-back Nick Shorey made great strides down the flank and pulled back a teasing cross that caused chaos in the Wolves defence.
Butler and goalkeeper Matt Murray missed the ball and Forster had time to control the ball at the far post before lashing his shot into the roof off the net from eight yards, sending 4,500 travelling Royals fans mental.
Luke Chadwick almost doubled the lead shortly after the break and the narrow escape finally sparked Wolves into life but they could not find a way past the impressive Hahnemann.
Forster's shot across the face of goal was just beyond the dispairing slide of Chadwick. Chadders was largely disappointing, doing very little to warrant his place in the starting line-up ahead of Glen Little and John Salako.
After Miller had dragged a shot wide in the 52nd minute, Hahnemann frustrated Wolves with two stunning saves.
Influential leading scorer Nicky Forster came off with a bang to the ankle on the hour mark and from that moment on the game swung in Wolves' favour. Fozzy is now extremely doubtful for the return leg.
First turning a 25-yard drive from George Ndah around the post and he then somehow got a hand on a powerful low shot from Miller nine minutes later.
But the pressure was slowly starting to build and Hahnemann was finally beaten 15 minutes from time.
The ball broke to Shaun Newton after Wolves appeals for a penalty following a challenge by Steve Brown on Paul Ince were turned down.
Newton latched on to the loose ball and drilled an angled drive that was bizzarely deflected past Hahnemann by Graeme Murty. The ball went first off Steve Brown and appeared to be goinjg out for a corner before Murty's unfortunate touch put the ball in.
Wolves sensed the chance to take an advantage into the second leg and did so when Ince was fouled on the edge of the area by Darius Henderson, and Naylor stepped forward to fire an unstoppable 20-yard shot past Hahnemann.
The Molineux side continued to press forward and could perhaps have had a third. Not even the late introduction of Jamie Cureton, magic boots et al could enable the Royals to swing the game once more.
The two sides meet again at the Madejski Stadium on Wednesday.