Chances were few-and-far-between throughout for the visitors and the result leaves Norwich four points above the drop zone in 15th, but the three teams below them all have games in hand.
Goals from Morgan Schneiderlin, Rickie Lambert and Jay Rodriguez helped the hosts into a comfortable 3-0 lead, but late strikes from Johan Elmander and Robert Snodgrass almost saw the Canaries stage an unexpected comeback.
Substitute Sam Gallagher wrapped things up for Southampton deep into stoppage time and, although elements of Norwich's fightback pleased Hughton, he was left disappointed on the whole.
"We rallied round really well at the end. We showed really good character and desire towards the end, but for too long we were second best," he told Sky Sports.
"We were up against a very good, a very mobile Southampton side with some very good players. But we needed to get closer to them.
"We needed to show more on the ball because I think if you're allowing a good Southampton side to have the possession they had, they can hurt you.
"If that's the case, then you can't concede the goals like we conceded the goals. I think in the first-half period, that was probably the best opportunity of the game.
"But we needed to show more on the ball, we needed to make more of a game of it."
Hughton made five changes to the side that drew 1-1 at home to Stoke and he concedes that it did not quite have the desired effect.
"That's the game," he said. "We made some changes today. I made the changes just to really freshen things up a little bit.
"We've got a lot of players that have played a lot of games.
"Our form at times has been disappointing and I think coming off the back of a result last week against Stoke - a game I felt we deserved to win - I decided to make some changes to freshen it up a little bit.
"With that, you're looking for an effect on the game. We were up against a very good Southampton side and we weren't able to do that today."