A late hotel change because of a ‘virus’ meant the Saints had to stay 40 miles away from the Liberty Stadium.
However, Southampton went on to beat the Swans 1-0 thanks to Manolo Gabbiadini’s late goal.
“It helped our focus,” said Hughes.
“We suspected that maybe some of the dark arts were at work but we didn’t let us affect us, in fact we used it as a motivating factor.”
The Marriott Hotel in Swansea defended its decision to cancel Southampton’s rooms, saying before Tuesday’s game it cancelled large bookings after some guests became ill.
Hughes stressed that he did not believe Swansea, who themselves needed to win the game to boost their hopes of starting in the Premier League, had a part to play in the incident.
“I’m not for one minute suggesting Swansea had anything to do with that,” he added. “Maybe it was over zealous Swansea fans in positions to affect our hotel booking maybe.
“But no, those things you can use to your own benefit and use as a motivating factor.”
The win moved Southampton up to 16th in the Premier League, three points ahead of Swansea who occupy the final relegation place.
Hughes’ side host Manchester City on the final day of the season on Sunday while Swansea are at home to Stoke but the Saints’ vastly superior goal difference means it would require a 10-goal swing for them to go down.
“I’m delighted for the club and obviously relegation is a huge negative, it’s not done mathematically but we’ve put ourselves in a good position,” Hughes added.
“We’ve come in and found a group of guys who needed bit more direction and a bit more belief. They’ve worked their socks off. I thought they were immense against Swansea and weren’t going to be denied.”
Swansea must now hope Huddersfield, who are three points above the relegation zone but with a worse goal difference, lose to both Chelsea on Wednesday and Arsenal on Sunday. If that happens, then Swansea will stay up with a win against already-relegated Stoke.
“In this moment we are not relegated,” Swansea boss Carlos Carvalhal said. “Definitely we don’t depend on ourselves.”
“I will not put the fault in my players, I never do this. I assume responsibility. It is not a question they are not good enough, we created chances. We did our maximum, the players did their maximum but we did not score for whatever reason.”