The former Rotherham striker proved decisive after coming on in the 64th minute, netting twice to help the Royals to victory in an intense Championship match the hosts had edged.
Reading goalkeeper Adam Federici produced a string of superb saves to keep Saints at bay throughout and Jason Roberts headed the visitors ahead after 19 minutes.
Rickie Lambert levelled three minutes into the second half as Southampton continued to press, although the second tier's sternest defence eventually overcame its mightiest attack.
Le Fondre put Reading back ahead in the 72nd minute and ended any doubt over Reading's fifth successive league win in stoppage time.
St Mary's was rocking as the match began and the noise went up a notch when talisman Lambert tested Federici from an acute angle.
While Noel Hunt had penalty appeals rejected at the other end, Saints dominated the early exchanges and Federici was again called into action to tip an Adam Lallana drive around the post.
The Reading goalkeeper was having to perform at his best to keep Saints at bay and soon thwarted another effort from Lallana, before reacting quickly to stop Lambert nodding home.
Danny Butterfield blazed wide as Nigel Adkins' side continued to press, although they fell behind out of the blue in the 19th minute.
Jimmy Kebe's superb cross from the right flank was met at close range by Roberts, who beat Jose Fonte to the ball and headed Reading in front.
Southampton looked for an immediate response to the goal and Lallana saw an exquisite goalbound chip tipped over the ball by Federici.
Jos Hooiveld headed wide from the resulting corner, before referee Mike Dean dismissed penalty claims from Billy Sharp that he was upended by Kaspars Gorkss.
Richard Chaplow picked up the evening's first booking in the 37th minute for a late challenge on Federici, but dusted himself down to produce a cross that Lallana prodded goalwards.
Lambert wasted a glorious chance to equalise in first-half stoppage time when he headed over at the far post, but made amends three minutes after the restart.
Sharp collected the ball in the box and pulled back for Lambert, whose venomous drive deflected off Gorkss and past Federici.
The Australian goalkeeper could do nothing to stop the strike but did brilliantly shortly afterwards to thwart an audacious effort by Chaplow, who was replaced moments later by Steve de Ridder.
Southampton were dominating possession and were defending sturdily on the rare occasions Reading ventured forwards.
Lambert came close from 22 yards and Ian Harte did well to block a De Ridder cross, before Lallana glanced a header wide.
Le Fondre came on in place of Jay Tabb in the midst of Southampton's domination as Reading boss Brian McDermott looked to alter the game's dynamics, with the move paying dividends in the 72nd minute.
Reading broke through and Kebe cut back for the former Rotherham striker to smash home into the top right-hand corner.
Federici saved efforts from substitutes De Ridder and Guly Do Prado as the clock wound down and Saints looked for an equaliser, with Lambert seeing a late penalty claim turned down.
Le Fondre wrapped up the three points in stoppage time, latching on to a misplaced Fonte header to round goalkeeper Kelvin Davis and net.