Lewington, the club's longest-serving player, is entering his 10th season with the Milton Keynes side and has put pen to paper on terms to keep him at stadium:mk until June 2015.
The 27-year-old left-back has been in discussions with the Dons throughout the summer as his contract was set to expire at the end of this month.
"It has been pretty close for the last two or three weeks so it is nice to know where I am going to be for the next few seasons and I'm glad it is all sorted," Lewington told the club's official website.
"It took a little longer than we would have all liked but at the end of the season you disappear off on your holidays and before you know it a few weeks have gone by. It probably dragged out a little longer than it needed to but we were talking and I was always confident of signing.
"It's nice to say I am part of this now; I can really focus on pre-season and kicking on with the season ahead. It will also help the gaffer with his plans for the team too. It's great to be a part of it and hopefully we can take the club where it wants to go.
"It's my 10th season so a testimonial is on the cards, but it will take a little while to work out and hopefully come Christmas I might know what we will do."
Dons boss Karl Robinson added: "I'm ecstatic that Dean has signed, he is this club through and through. I never thought at any stage that he wouldn't be here next season.
"He is a tremendous asset to this football club and one of his ambitions is to play in the Championship with MK Dons. He deserves all of the plaudits that he gets and I hope one day he gets the success that his loyalty deserves.
"In modern day football it is a great achievement to be heading into his 10th season with MK Dons, but knowing Dean as a character it doesn't surprise me. He has a dream and a goal with this football club, he has started it and he wants to achieve it."