The Royals were trailing at Millwall thanks to Andy Keogh's early strike, but Hal Robson-Kanu fired them level seconds before the break.
And in the second half, with the lowly Lions waiting for an offside flag which never came, Le Fondre tucked in Jason Roberts' cross to leave Reading just a point behind second-placed West Ham, who play at Cardiff on Sunday.
Portsmouth's 10-point deduction may have eased Millwall's worries at the foot of the table, but their financial crisis could also have a significant impact on Reading at the top.
Should Pompey go bust before the end of the season and their results are wiped off the records, the Royals would gain six points on West Ham.
Either way Brian McDermott's side are charging like a train towards the automatic promotion spots.
But they looked out-of-sorts for the majority of a tetchy first half, which suited Millwall in front of a vociferous home crowd who howled each time so much as a throw-in decision went against them.
In the 15th minute the hosts' pressure told when Harry Kane lofted the ball over the Reading backline and Keogh slid it past the advancing Adam Federici and into the net.
It was the first goal the Royals had conceded in 490 minutes, and only Millwall's second at home in the league since the turn of the year.
They nearly made it two when Federici spilled Hamer Bouazza's fierce cross-shot but Keogh could not quite turn in the loose ball.
Reading did not muster a shot on goal until five minutes before half-time, Ian Harte driving a 20-yard free-kick over the top.
But their second effort turned out to be a spectacular equaliser.
In the third minite of injury time, Millwall gave a way a comical corner when Bouazza's attempted clearance rebounded off Tony Craig's backside.
David Forde got a fist to Harte's cross but could only punch it as far as Robson-Kanu, who thumped a superb volley back past the Lions keeper and high into the net.
Millwall should have gone back ahead after an hour but Kane somehow missed James Henry's cross with the goal gaping.
Instead, Reading grabbed the winner with 15 minutes remaining.
Le Fondre knew he was offside when Mikele Leigertwood thumped the ball forward, but the wily Roberts was not and took the ball on as Millwall stood with their hands in the air.
The flag never came and Roberts laid the ball into the path of Le Fondre who made no mistake at the back post to make it six of the best for the Royals.