Le Fondre, who is on a season-long loan from Cardiff, made amends for a glaring miss just moments earlier when he converted an 85th-minute cross from Benik Afobe as Wolves ended a run of back-to-back league defeats.
However, they did it the hard way as Charlton – who lost for the first time in the Championship this season – took a 55th minute lead through Johann Berg Gudmundsson.
Welsh international midfielder Dave Edwards got his second goal of the season 10 minutes later to draw Wolves level, before Le Fondre completed the comeback.
Wolves, who were without long serving central defender Richard Stearman ahead of a proposed £2million move to Fulham, made a sparkling start when they should really have taken the lead.
Afobe, who has been the target for three bids from Norwich this month, set up winger James Henry – whose curling shot from the edge of the area drifted just wide.
Henry, the target of an approach from Charlton earlier in the summer, turned provider four minutes later with a cross that Edwards headed over the bar.
Henry was proving to be a constant menace to the Charlton defence and, after another of his crosses had proved inches too high for Nouha Dicko, he tested Charlton goalkeeper Nick Pope – who was relieved to tip his 20-yard drive over the bar in the 17th minute.
Charlton’s bid to gain a foothold in the game was not helped 60 seconds later when their giant Danish striker Simon Makienok limped off with a hamstring injury.
When Charlton did finally mount an attack they failed to test goalkeeper Carl Ikeme on the half hour when Gudmundsson dragged his long range shot well wide.
Jordan Cousins was also well off target on the stroke of half-time when his drive flew well over Ikeme’s crossbar.
The failure of Wolves to make their pressure pay at the start of the match came back to haunt them at the beginning of the second period when Gudmundsson broke the deadlock.
The Iceland international found himself unmarked on the left hand edge of the Wolves area and after collecting a pass from Igor Vetokele he drilled a low shot under the despairing dive of Ikeme – his second goal in successive games.
Wolves were completely rocked back by the shock of falling behind and they were lucky not to slip further adrift three minutes later when Zakarya Bergdich flashed a shot across the face of goal.
The home side’s hopes of launching a comeback were not helped after 62 minutes when Dicko was carried from the pitch on a stretcher with an ankle injury.
However, they quickly made light of that setback when Edwards cashed in on a right-wing cross from substitute Sheyi Ojo to bundle home a close-range shot past Pope.
Wolves looked to have blown their chance to win the game when Edwards headed over the bar from six yards in the 76th minute, then Le Fondre blazed his shot over the bar five minutes later.
However, with time running out the 28-year-old former Rochdale, Rotherham and Reading made amends by steering home Afobe’s cross to give Wolves all three points