The second-half strike from the centre-back, which was hacked away too late after it crept over the line marginally, was one of numerous efforts that Saints hit throughout the encounter.
Southampton struck the woodwork twice, Jay Rodriguez with a curling effort from 25 yards that crashed off the crossbar before Jack Cork nearly capped his 100th league start for the visitors in fine fashion with a drive from similar distance that bounced back off the post.
The Tigers rarely threatened to find the net themselves and came closest through Shane Long’s glancing header onto the far post – the only moment of concern for Saints as they comfortably extended their unbeaten run in the league to eight matches.
Mauricio Pochettino’s side eased into early domination, Rodriguez cleverly flicking Adam Lallana’s pass beyond an onrushing defender before failing to reach the ball as Stephen Harper smothered.
That piece of play preceded a glorious opportunity, again provided by Lallana that brought Southampton within inches of opening the scoring through Rickie Lambert.
The forward calmly controlled and shifted the First Team Captain’s cross before slamming it against the top of the stanchion behind the net.
Another inviting chance was presented to Lambert in the eighth minute when he met Steven Davis’ defence-splitting through-ball with an attempted chip that Harper prevented with his right arm before it flew over him.
Hull defender Paul McShane was injured in the process of trying to stop Lambert’s lifted effort and was forced to be replaced by George Boyd, whose first involvement came in the hosts’ first attack of the encounter.
Following the unmarked Rodriguez’s header from Lallana’s corner that was cleared off the line, Shane Long’s glancing nod from Ahmed Elmohamady’s cross proved to be much more dangerous as it bounced off the post and ricocheted out to Boyd.
The winger failed to make the desired contact with a first touch since his introduction, drilling the ball into the ground and allowing Artur Boruc to recover and comfortably tip the looping hit over the crossbar.
Rodriguez’s persistence had the woodwork shaking at the other end soon after the half-hour mark. The forward was afforded ample space 25 yards from goal which allowed him to whip a curled effort that rattled the top of the goalframe.
The Tigers were restricted to much more speculative but less frequent attempts, Jake Livermore providing Hull’s first try since they hit the post with a 35-yard volley that soared high and wide.
Nikica Jelavic fashioned his first glimpse of goal as half-time approach as he snuck into the box before using the outside of his foot to knock a fairly tame effort into the grateful arms of Boruc.
Harper had cause for concern on two occasions in a fast-paced end to the half that brought no breaking of the deadlock. The ‘keeper parried away a fizzing Luke Shaw cross through the six-yard box before avoiding a scare in the last action of the half as Rodriguez met another cross from the left flank at the back post with a header that flew over.
HALF-TIME: HULL CITY 0-0 SOUTHAMPTON
The restart seemed to prompt an audacious streak in both frontlines, Jelavic trying his luck from 30 yards as he swung a free-kick into Boruc’s grasp before Rodriguez acrobatically leapt to meet Calum Chambers’ cross for an overhead kick but the execution failed as he shinned it off-target.
Saints’ pressing continued as a quick passing exchange with Lallana followed the ever-present Rodriguez’s surge down the left wing before the latter was flagged offside as he prodded straight at Harper.
Relentless pressure from the visitors eventually paid dividends when a goalmouth scramble resulted in FONTE hooking the ball marginally over the line before it was cleared away.
Several attempts, one of which was a header from the goalscorer, were cleared before the ball deflected into Fonte’s path for a side-footed effort that crept over the line. Lambert fired in to ensure Saints had the lead, although the goal had already been awarded to the Portuguese.
Hull failed to muster a strong response, substitute Sone Aluko’s scooped free-kick into the stands epitomising their lack of threat.
Another substitute, Guly, nearly enjoyed more luck when Shaw’s shot that was destined for the far corner was parried into his path. The change in direction took the unsuspecting Brazilian aback slightly as he failed to re-adjust his body for a proper connection with the ball, allowing Harper to block his scuffed follow-up.
Cork came painfully close to rounding off the performance in style with a 25-yard effort that smashed against the post with Saints closing out the narrow victory strongly.
FULL-TIME: HULL CITY 0-1 SOUTHAMPTON
Hull City team: Steven Harper, Paul McShane (George Boyd 12), Maynor Figueroa (Robbie Brady 75), Alex Bruce, Curtis Davies, Tom Huddlestone, Jake Livermore, Ahmed Elmohamady, David Meyler (Sone Aluko 75), Nikica Jelavic, Shane Long.
Unused Substitutes: Eldin Jakupovic (GK), Stephen Quinn, Robert Koren, Yannick Sagbo.
Southampton team: Artur Boruc, Calum Chambers, Jose Fonte, Maya Yoshida, Luke Shaw, Jack Cork, Morgan Schneiderlin, Steven Davis (Victor Wanyama 90+2), Adam Lallana (c) (James Ward-Prowse 88), Jay Rodriguez, Rickie Lambert (Guly 76).
Unused Substitutes: Kelvin Davis (GK), Nathaniel Clyne, Jos Hooiveld, Lloyd Isgrove.
Goal: Fonte (69)
Bookings: Shaw (45+2), Fonte (48), Schneiderlin (82)