Saints were good value for three points, maintaining a fierce tempo throughout at the KC Stadium and creating a host of fine chances.
Rickie Lambert and Jay Rodriguez were both in profligate mood, raising Hull's hopes of a battling draw, but Fonte settled things in the 69th minute when he stabbed over the line at the second attempt.
The Portuguese defender needed the Goal Decision System to claim the goal, with Lambert rifling home on the follow-up after Maynor Figueroa tried in vain to clear the danger. However, other replays later suggested Saints shouldn't been awarded the corner which led to the goal.
Lambert had earlier missed a pair of wonderful chances in the opening seven minutes, while Rodriguez struck the crossbar from 20 yards.
Hull were far from passengers in the contest, striking the woodwork first when Shane Long's header kissed the inside of the post, but they could not match Saints' energy around the park and tired visibly as the game progressed.
Having taken four points from Tottenham and Sunderland this month, their attempts to pull clear of the strugglers were duly stalled.
Adam Lallana wasted no time in carving out an early chance for Saints, exchanging passes with left-back Calum Chambers before clipping a cross from the byline.
Curtis Davies deflected into the ball into Lambert's path and he looked certain to score, only to shoot a yard wide from 12 yards.
With time and space, he should have done better.
That miss might still have been on his mind three minutes later when Steven Davis' precision pass presented an equally good chance.
Having timed his run to perfection Lambert took a slightly heavy first touch, allowing Steve Harper to close the angle and save with his legs.
In doing so the veteran keeper clashed with team-mate Paul McShane, with both men needing treatment before the latter was taken off on a stretcher.
Hull collected themselves in the break of play and, with no natural defender on the bench, sent on George Boyd in a revised 3-5-2 formation.
The change almost paid immediate dividends when Ahmed Elmohamady found Shane Long in the Southampton area in the 13th minute.
The Irishman leapt highest and was unlucky to see his header come back off the inside of the post.
Boyd was following up for the rebound but the ball would not settle for him and Artur Boruc was able to tip over comfortably.
Things continued at a lively pace and on the half-hour mark, Southampton again came close.
Hull failed to close down Rodriguez 20 yards from goal and he proceeded to lift a delicate shot out of Harper's reach but flush against the crossbar.
Saints were playing with considerably more craft than their hosts, but Jake Livermore's long-range strike and Nikica Jelavic's pick-pocketing of Fonte kept Hull in the argument.
Rodriguez almost nicked the opener in the final seconds of first-half injury time, but could not keep his far-post header down after good work by Lallana.
Hull were firmly on the back foot after the restart.
Rodriguez tried and failed to execute a bicycle kick at the far post, Luke Shaw breezed past David Meyler and Elmohamady in one swift movement and Lambert worked Harper having met Davis' deft pass.
But for all their superiority, Southampton were struggling to find a finish to match.
Hull were quickly settling into a siege mentality, though the decision to leave both Jelavic and Long up front did mean that the visitors could not afford to switch off at the back.
The home side's defence eventually buckled with 21 minutes remaining but not without a major fight.
Harper played his part, getting down well to keep out Fonte's headed effort and then recovering to make a point-blank block as Lallana attempted to bury the rebound.
The ball squirmed loose and returned to Fonte, whose side-footed effort crept over the line despite Figueroa's best efforts.
Goalline technology confirmed the ball had crossed but it would not have affected the scoreline, with Lambert netting unequivocally seconds later.
Either side might have scored in a frenetic closing period, but somehow the ball stayed out.
Shaw left Harper at full stretch with a skiddy effort that looked destined to creep in, and Jack Cork struck the outside of the post as Saints attempted to put the game to bed.
Jelavic or Sone Aluko's chances for Hull were less clear-cut but both gave the home fans cause for late excitement on an otherwise disappointing night.