Referee Martin Atkinson had to refer to the Goal Decision System in order to finally award Southampton the goal after the ball looked to have been hacked off the line.
There was initial confusion over who scored it as Fonte's effort was cleared as far as Rickie Lambert and he rammed home the rebound before the goal-line technology awarded it to the Portuguese defender.
Shane Long had earlier been denied by the frame of the goal on what was a disappointing evening for Hull, who also lost defender Paul McShane to injury in the first half.
Victory for Southampton moves them up to eighth above Newcastle United, while Hull are still three points from the drop zone after their fourth home league defeat of the season.
Steve Harper continued in goal for Hull in place of the suspended Allan McGregor, while Gaston Ramirez and Dejan Lovren both missed out for Southampton.
It was the visitors who started brightest, Lambert pouncing on to a deflected cross from Calum Chambers on the right before shooting wide with four minutes gone.
Lambert again caused problems when he was played through by Steven Davies, but his heavy touch gave Harper and McShane enough time to react to his attempted effort on goal.
However, Republic of Ireland defender McShane had to be carried off on a stretcher and was replaced by George Boyd as a result of the three players colliding after just 12 minutes.
Shortly after the restart, McShane's international team-mate Long struck the post for Hull with a headed effort from the centre of the box after meeting Ahmed Elmohamady's dangerous cross.
Full-backs Elmohamady and substitute Boyd continuously tested the Southampton defence with deliveries from both wings.
Jay Rodriguez then came close to putting Mauricio Pochettino's side ahead after 30 minutes when his curling effort from outside the box beat Artur Boruc, but hit the crossbar.
Nikica Jelavic tested Boruc five minutes before half-time with a right-footed shot as he made the most of a failed clearance following another Elmohamady cross.
Hull were the first to threaten after the restart, but Jelavic's long-range free-kick was easily saved by Boruc.
Rodriguez then failed with an acrobatic attempt at goal from close range after good build-up play from Luke Shaw on the left wing.
Southampton started to dominate and the constant pressure nearly paid off as Lambert almost opened the scoring with a shot from a tight angle inside the box.
However, the visitors did take the lead with just over 20 minutes remaining.
Harper failed to deal with a long ball in from Chambers and Fonte's reaction shot then looked to have been cleared off the line, but referee Atkinson gave the decision in Southampton's favour after a referral to goal-line technology.
Hull failed to make an impact on the game after the goal as they suffered a setback at the KC Stadium.
