The striker's clinical second-half double, coming after Rickie Lambert had cancelled out Jason Roberts' headed opener, sent Royals three points clear at the top of the Championship.
And with third-placed West Ham now nine points off the pace with just four games remaining, Brian McDermott's men are on the brink of a return to the top flight.
Fittingly, victory at a sold-out St Mary's, Royals' 14th triumph in their last 16 outings, was earned not through individual brilliance or a stunning strike, but through grit, team work and pure determination.
From the off, the visitors were under the cosh, with Saints peppering the Reading box with crosses and also threatening through the impressive Adam Lallana.
But for all their early dominance, as well as the problems posed by the imposing striking duo of Rickie Lambert and Billy Sharp, Southampton found themselves behind midway through the half.
After a misplaced Saints' pass, Hayden Mullins spread the ball to Jimmy Kebe on the right, who lofted a deep cross into the box that Roberts headed home from close range.
The goal sparked wild celebrations amongst the large contingent of travelling fans, yet it didn't galvanise Royals into taking control of the match.
Still Saints dominated, with Adam Federici tipping an audacious Lallana chip over the bar and Daniel Fox heading wide from the resulting corner.
But Royals, despite being on the back foot for most of the half, held out until the break.
Unfortunately for McDermott's men, it took Saints just a couple of second-half minutes to draw level.
A ball into the box from the left was chested down by Sharp into the path of Lambert and his shot deflected off Kaspars Gorkss and over a diving Federici.
With the wind in their sails, Saints looked favourites to get the next goal, and both Chaplow and Jos Hooiveld went close.
But again the Reading defence held firm, and the visitors regained the lead in the 73rd minute when substitute Le Fondre finished off a neat move he started in midfield by smashing Kebe's cross into the roof of the net.
With time running out and their noses in front, Royals were content to sit back, confident in their ability to see out the remainder of the match.
And not only did they do that, but they put gloss on the victory late on when Le Fondre showed brilliant persistence to nick in and steal Jose Fonte's back pass before taking a touch around goalkeeper Kelvin Davis and scoring.
Next up for the Royals is a home game against Nottingham Forest on Tuesday evening (8pm ko).