The Royals finally recorded their first win of the campaign in their 11th outing to move up to 17th position on the table as the Toffees lost for just the second time in the league this campaign.
The Scottish striker made it 1-0 to Everton in the 10th minute when he prodded home from close range after Nikica Jelavic's lofted ball into the six-yard box was not dealt with well by Royals defenders.
But Brian McDermott's men picked themselves up after going a goal down and managed to equalise six minutes into the second half when Le Fondre headed home Nicky Shorey's free-kick from the left.
The former Rotherham man then edged Reading ahead with just under 20 minutes remaining when he sent Everton keeper Tim Howard the wrong way from the penalty spot after Seamus Coleman had clattered into his back in the area.
The spot-kick was the eventual winner for Reading as they dusted themselves off after a mediocre beginning to the season to show they can mix it as David Moyes' Toffees had a minor blip on what has been an otherwise positive radar thus far.
Madejski Stadium, Reading - 24,184