Burnley took a shock lead after 19 minutes on Wednesday night when Robbie Blake volleyed home superbly after a spell of pressure from the hosts.
United could have levelled just before half-time when Blake brought down Patrice Evra for a penalty, but Burnley goalkeeper Brian Jensen turned away Michael Carrick's spot-kick.
And while Ferguson believes United were the better side for the bulk of the game, he admits they did not perform to the best of their abilities.
"We're disappointed," he told Sky Sports.
"It wasn't a great performance by Manchester United but, saying that, maybe it was just a night for Burnley.
"They've been out of the Premier Division for 30-odd years - maybe it was their night because so many things happened in that penalty box it was just amazing we didn't get one.
"Maybe if we'd scored the penalty just before half-time we'd have gone on to win but, nevertheless, you can't deny them the victory. They've been a long time out of the Premier Division."
He added: "For ten minutes in the first half, they played very well and put the ball in the box a lot with some terrific crosses and they were a real threat to us.
"The goal by Blake was a fantastic hit. We didn't defend it well and we should have been back goal-side of the lad, but it was a great strike.
"From there on, it was complete domination and in these situations, with our experience, we should have been doing better."
Penalty missCristiano Ronaldo had previously been United's undisputed penalty taker, but Ferguson felt confident in Carrick and has no qualms about the miss.
"There's one or two that have been taking penalty kicks over the last two or three years and Michael's one of them," he said.
"He felt confident so I've no problem with that."
Michael Owen, meanwhile, was given his first start for United but was substituted on 63 minutes after a disappointing showing in which he passed up two good chances.
Ferguson accepts that the striker has yet to show his best form for the club but believes he just needs to regain his sharpness.
"I think he's probably in need of two or three games," he said.
"I think that'll help him."