Portuguese Fonte responded to the upheaval in the best way possible, with his 69th minute winner his second goal in four matches after he scored the opener in the 2-2 draw with Arsenal.
The win allowed Southampton to move into eighth spot ahead of Newcastle's match with Tottenham Hotspur on Wednesday, and manager Mauricio Pochettino said the solidarity shown by the team since the Osvaldo incident was standing them in good stead as they extended their unbeaten run to eight matches in all competitions.
"That is completely forgotten, in the past, and we can only look forward," he said.
"The group mentality, the team, is the most important thing, that there's no player above the team and we will always defend the common interest of the group and not a single player."
Rickie Lambert, Jay Rodriguez and Adam Lallana were again prominent as Southampton largely dominated the encounter, a lack of cutting edge in front of goal meaning they were unable to secure the result earlier.
Hull's Shane Long did hit the post in the first half, as did Southampton's Jack Cork late on but Fonte's effort, after a goalmouth scramble and the intervention of the Goal Decision System, was just reward for the Saints' endeavours.
"We put in an amazing shift," Pochettino told the BBC.
"We dominated the entire game from start to finish. We're very happy with the performance. The entire team always plays for each other. That's the Southampton way.
"It's very important we take it game by game. We focus on the next game ahead. Now we'll be focusing on the FA Cup game away at Sunderland, which is an important match."
(Reporting By Josh Reich; Editing by John O'Brien)
