Boro came into the game more after the break, yet Preston hit the post through Ross Wallace and saw strong appeals for a penalty waved away before Jonathan Franks added the Teessiders' second late on.
North End are now without a victory in six away games, but Ferguson said: "We deserved to win. I thought we were excellent.
"I'd rather play badly and win, obviously, but I thought my players' performance was top-drawer.
"I can't really have any complaints about any of my team and I've just said to them in the dressing room, if we can play to that standard we've got a good chance of winning most of the seven games we have left.
"But it's still no consolation, it's another game we've lost."
The Lilywhites boss added: "I felt for a large part of the game we dominated. But we just didn't get the goal and then we've lost a really sloppy goal which has given them something to hang on to.
"That's the main disappointment of the night, because it's a soft goal for me and we're conceding far too many soft goals."
When asked about his side's second-half penalty claim, which came after Darren Carter had gone down under a challenge from Stephen McManus, Ferguson replied: "It doesn't matter. The referee hasn't given it.
"It looks to me as though he was going to blow his whistle. I asked him about it and he said the linesman was in a better position, but the referee's five yards away and the linesman is 35 yards away.
"I think it's a penalty, but he hasn't given it."
Middlesbrough boss Gordon Strachan was relieved to come away with three points after seeing his squad decimated by a combination of injuries and a virus sweeping the club.
"We've had a traumatic couple of days with injuries and illness and the team got changed this morning three or four times," he said.
"The victory had nothing to do with football really, but a lot to do with drive, determination and a will not to get beat.
"Preston must feel unfortunate, but it's the only time I can say we've had a real bit of luck.
"It was a team that was thrown together and we didn't get going at all, but I thought the three substitutes (Kyle Naughton, Andrew Taylor and Leroy Lita) did very well for us."