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.
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. Full coverage of today's matches can be found on the ITV Sport website here.
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.
James Ward-Prowse, one of three 18-year-old academy graduates in the starting line-up, sent over a looped cross to Lambert, with only an exquisite Westwood save down to his right preventing the England international heading home.
Ironic cheers met referee Lee Mason's award for a foul on the new boy late on - a decision that led to Saints equalising at the death.
Ward-Prowse floated in the free-kick and centre-back Fonte met the ball with a powerful header that at last beat Westwood.
Rodriguez saw a shot deflect wide as Saints pushed for another in stoppage time, but there was to be no further goals.
After Southampton revealed the Italy international had put pen to paper on a four-year deal, his former employers in the Italian capital released the details on a deal initially worth £12.9m. That figure could rise by another £1.7m dependent on Osvaldo's performances at St Mary's.
The fee for the 27-year-old, who is due to be presented to the media tomorrow, exceeds the £12.5million they forked out last month to bring midfielder Victor Wanyama from Celtic.
Osvaldo worked with Southampton manager Mauricio Pochettino when the pair were at Espanyol, although getting him to the south coast took some persuasion.
"Southampton football club is delighted to announce the signing of Italy striker Pablo Daniel Osvaldo," a statement on the club's official website, www.saintsfc.co.uk, said.
Osvaldo, who has nine Italy caps, becomes Southampton's third signing of the summer, following an £8.5m move for Lyon defender Dejan Lovren and the signing of Kenya midfielder Wanyama.
Southampton won their opening match of the season at West Brom on Saturday, with a late Rickie Lambert penalty securing a 1-0 victory.
Rickie Lambert's 35th-minute free-kick proved enough to seal a 2-1 win at St Mary's after an early opener from Jay Rodriguez had been cancelled out by a header from John Terry.
Chelsea's shock loss allowed Tottenham to leapfrog into third place with a 2-1 win at Swansea.
The Potters, who had not registered a Barclays Premier League victory since Boxing Day, were in control for virtually the entire contest and finally broke down their opponents' stubborn resistance in the 67th minute when Huth nodded home a Glenn Whelan corner.
Substitute Jerome then cracked the ball in with nine minutes of normal time remaining having taken the ball down neatly and turned his marker. Adrian Mariappa pulled one back with a header two minutes later.
The Royals - who have scored a host of important late goals in recent weeks in an unbeaten sequence of four league games - could not complete a last-gasp fightback on this occasion. They remain 17th in the table, two points clear of the relegation zone, while Stoke stay 10th.
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