The talking point of the game saw Englandbeing denied an equalising goal just minutesafter, when a Frank Lampardshot from 20metres hit the crossbar before bouncingdown over the line.
Reading did threaten when Long headed John Oster's free-kick wide and Matejovsky fired in abouncingshot that City keeper Joe Hart did well to push away.
Peter Odemwingie sent ashotbouncing wide with Hart scrambling across his goal and, after Brunt blasted over, substitute Fortune fired into the side-netting after running clear and Carlos Vela headed wide when well placed.
Having rarely threatened before the interval, St Mirren unexpectedly levelled in the 48th minute as Killie failed to deal with abouncing ball and Thomson took full advantage by slamming a low shot into the net from close range.