The former Rotherham striker proved decisive after coming on in the 64th minute, netting twice to help the Royals to victory in an intense npower Championship match the hosts had edged.
Reading’s Australian 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, latching on to a superb cross by Jimmy Kebe
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 wrapped up the three points in stoppage time, latching on to a misplaced Fonte header to round goalkeeper Kelvin Davis and net.
The result now sees Brian McDermott’s Reading move three points clear of their promotion rivals, who are a further six points clear of third-placed West Ham, who face Brighton today.