Despite leading from the fourth minute, Nigel Adkins' team were on the verge of their sixth defeat in seven games after Fulham's second half revival. However, Fonte's 90th minute leveller earned the Saints a point.
The Portuguese defender opened the scoring in somewhat fortunate fashion as Adam Lallana's near post corner came off his shoulder and looped inside the far post early on.
Substitute Jos Hooiveld inadvertently brought Fulham back on level terms as he diverted John Arne Riise's low drive into his own net with twenty minutes remaining.
Two minutes from time Kieran Richardson looked to have clinched the points for the visitors when he side-footed Sascha Riether's cross home with the aid of another deflection off Hooiveld.
Daniel Fox was the provider for the equaliser when his delivery from a free-kick found Fonte amongst a crowd of players and the defender steered his header down into the bottom corner as the match moved into stoppage time.
The result sees Fulham consolidate their good start to the season as they remain in ninth position while Southampton move out of the bottom three with their fourth point of the campaign.