The Saints were the better side for the majority of the match, and finally got the goal their dominance deserved, with Fonte smashing in the rebound after a wonderful double save from Hull goalkeeper Steve Harper.
There was some doubt as to whether the ball had crossed the line, with Rickie Lambert making sure Saints would go in front as Fonte celebrated, but the goal was later confirmed to be the Portuguese defender's.
Mauricio Pochettino's men were good value for their win having hit the woodwork twice in the match, with the home side struggling to break down a rigid Saints backline.
The visitors moved up to eighth as a result, and are now eight unbeaten in the league.
Hull however must start to look over their shoulders with several of their relegation rivals still to play on Wednesday.
Southampton came out of the blocks at a frenetic pace, and their speed on the counter-attack was causing the home side all sorts of problems right from the word go.
Lambert really should have broken the deadlock as early as the fourth minute after Adam Lallana's deflected cross found him in space in the box, but after doing brilliantly to control the bobbling ball, the England international somehow side-footed wide from eight yards.
Lambert then went close again, but elected to try and chip the onrushing Harper when put through, and the veteran 'keeper smothered well.
With their first real attack the home side could have gone in front, but Shane Long's glancing header came back off the post with Saints goalkeeper Artur Boruc beaten.
Jay Rodriguez was next to hit the frame of the goal, curling a fantastic effort from 25 yards goalwards only to see it come back off the crossbar.
After the interval the match was far less frantic, with a couple of acrobatic Rodriguez efforts the best opportunities spurned.
Long and Nikica Jelavic toiled away up front for Hull, but they weren't getting the service they needed to get on the scoresheet again.
And it was a Southampton defender who snatched all three points, converting after fantastic goalkeeping from Harper.
From a debateable corner, Fonte's initial header was well saved by Harper, who then brilliantly kept out Lambert's rebound, but after another blocked effort the ball fell to Fonte again, who beat Harper to score, despite Maynor Figueroa's efforts on the line.
There was still time for Jack Cork to hit the crossbar again with an effort from distance, but one goal was enough for Pochettino's men to maintain their good form and keep alive their hopes of a top-six finish.