Wayne Rooney scored twice on a threadbare pitch to seal the points for United after Jay Rodriguez had punished a mixup between Michael Carrick and keeper David de Gea to put Southampton ahead after three minutes.
Rooney's first goal was his 100th at home for United but it did not disguise a lethargic performance from his team-mates who were merely hanging on before the final whistle.
Ferguson was full of praise for Southampton who were impressive under new manager Mauricio Pochettino but clearly unhappy with the lack of grass on the pitch.
"In the second half, the players just found the pitch impossible," Ferguson, whose side moved seven points clesar of Manchester City, told the club's website.
"We tried to play the way we normally play and found it difficult because the pitch had dried out a lot. It was an ice cold night and it happens.
"We lost an early goal but it didn't deter us from playing some fantastic football and we could have been four or five up at half-time, but once the pitch started to dry out the players found it difficult to play a different way and it really required us to play the ball into the gaps, which we don't normally do.
"For the first 30 minutes I thought we were fantastic, we played really well," he added. "But in the second half Southampton have been the best team to play here this season. We were fortunate to win the game.
"The pitch didn't help us. We can't use that as an excuse, but it didn't help us. It's a worry."
Pochettino, who surprisingly replaced Nigel Adkins whose sacking drew words of support from Ferguson in the matchday programme, said the praise was welcome.
"I'm very proud [of Ferguson's praise]," he told the BBC through an interpretor. "It's very important for my players to hear. But we leave with no points.
"We did play well but I'm upset at not getting a draw at least. It doesn't console me."
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