Romelu Lukaku scored the only goal of the game with just 20 minutes on the clock, with United seemingly content to sit back thereafter as they registered fewer than two goals in a game for the first time this season.
Saints did apply the pressure as the game drew to a close, with Oriol Romeu coming the closest to finding a late equaliser, but United held firm for all three points on a frustrating afternoon for Long.
"I thought we deserved more from the game. Manchester United are dangerous all over the pitch," he told Sky Sports News.
"They have physical players on set pieces. To limit them to one goal was a credit to our team but it was just a shame we couldn't get that equaliser at the other end.
"There were a lot of chances but things didn't seem to fall for us. It wasn't through a lack of trying though. It just didn't happen today."
Next up for Southampton is a trip to Stoke City next Saturday.