St Ledger was Preston's player of the year in 2008 and will add competition to Middlesbrough's defence.
Boro's defensive record this season is one of the strongest in the Championship, having conceded only three goals in six games - while Preston have let in one more.
Preston chairman Derek Shaw told BBC Radio Lancashire the club had little option but to let St Ledger move on.
"My honest view is if we don't do this type of thing we'll be getting 10 points deducted and we'll end up going into administration," he said.
"Everybody saw the Southampton situation in the summer. They've seen it at Derby and at Bradford and we don't want it to happen here.
"With our gates and the turnover of the football club we're competing against some very big clubs, but we always seem to get onto the same subject where money is everything in the game.
"Middlesbrough have got parachute money, they've bigger gates than us, they've just been relegated from the Premier League and they have a chairman who can afford to back up their losses."
Manager Alan Irvine admitted he did not want St Ledger to leave, but understood the reasons.
"I am disappointed and I didn't want Sean to go but I understand what effect money has both in terms of clubs and players and I accept Sean has gone and we have to move on.
"I have thoroughly enjoyed working with him and Middlesbrough have got a really good player. I think he'll continue to improve and go on to be a top player."
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