The Bosnia international scored after his wind-assisted hoof downfield took a huge bounce over opposite number Artur Boruc to give the Potters the perfect start only for Jay Rodriguez to equalise just before half-time.
"It was a fortunate goal, quite bizarre really, and we were grateful for it," said Hughes, who celebrated his 50th birthday on Friday.
"I think he just wanted to get his foot through it. You could tell as soon as the two centre-halves made the decision to let it bounce the goalkeeper was going to be in trouble because it took a hop, skip and a jump and he was never going to get anywhere near it.
"I don't think I've ever seen a goalkeeper do that, which was great for us.
"Obviously the idea in the first half was to take advantage of the conditions but unfortunately conditions spoiled the game.
"We wanted to get on the scoresheet first because it is common knowledge if you score first in the Premier League statistically you have a better opportunity of winning games.
"We weren't expecting our goalkeeper to do it for us but give him credit it was a great strike and he is very pleased with it. He is looking to score a few more he tells me.
"We turned them around to try to take advantage of the conditions but in hindsight the wind was more difficult to play with than against.
"I thought Southampton were the better side in the first half and I thought we edged it in the second half against the wind in terms of chances.
"The wind wasn't great for both sides in the end and I felt the game was a draw and both teams will be comfortable with that."
Southampton boss Mauricio Pochettino apportioned no blame to Boruc and put the opening goal down to bad luck.
"As a manager that is the first time I've had to experience a moment as unlucky as that," he said.
"I don't blame him (Boruc) at all. I think it had more to do with the weather conditions, it was something completely unexpected, but we are aware these things can happen in football.
"He didn't apologise for anything because he didn't have to.
"The wind was changing gusts completely all the time and it is a ground which is open on three sides which makes it even more windy.
"It was a really tough game in terms of the weather conditions."