It had looked like an early goal from the diminutive Emanuele Giaccherini would see Paolo Di Canio's men take three points back to the north east.
Standing at just 5ft 5in, the smallest player of the pitch headed home a Sebastian Larsson corner unmarked in just the third minute.
Poor finishing, fine goalkeeping from Kieren Westwood and plain old bad luck looked set to deny Saints, only for centre-back Fonte to head home two minutes from time.
It was just reward for Mauricio Pochettino's side, who came into the clash buoyed by a fine opening-day win at West Brom and another big-money acquisition.
Following moves for Dejan Lovren and Victor Wanyama, Dani Osvaldo arrived this week from Roma for a fee that could reach £14.5million.
The forward was named amongst the substitutes at St Mary's, where another Italy international struck the first blow.
Larsson sent across a corner from the left found Giaccherini unmarked and he nodded home to the delight of the hardy 1,867 travelling fans.
It was hardly the start Southampton wanted but one they responded well to. Rickie Lambert slipped through a fine ball to Jay Rodriguez, who slotted past Westwood and wheeled away in celebration - only for the linesman to rule the sixth-minute leveller out for offside.
Saints again came close 10 minutes later, with Westwood this time the man in the way.
Source: PA
Source: PA