The Sheffield Wednesday defender had been on loan with the Dons and has now made his move permanent.
The deal sees him remain at Aberdeen until the summer of 2017, while goalkeeper Dan Twardzik has signed an 18-month contract after being granted international clearance.
Reynolds first joined Aberdeen on loan in the January transfer window last year, before returning in the close-season on a season-long deal.
His permanent capture was a priority for boss Craig Brown this month, with no further business expected ahead of tonight's deadline.
Dons chief executive Duncan Fraser told the club's website: "Craig's key objective for some time has been to sign Mark on a full-time contract.
"The length of the deal reflects the fact the player very quickly established himself as part of the backbone of the squad here and, despite the fact he is still only 25, he is very much regarded as one of our senior players with a wealth of experience under his belt."
Reynolds said: "After a spell of uncertainty, it's great to get my future sorted out and know that I'm going to be in the north east for the foreseeable future. My family settled in Aberdeen very quickly and we really like the area and, with the recent birth of our son Lucas, it's a huge boost to know that we'll be staying here.
"It's up to me to repay the faith the club has shown in me and I do believe we have a squad capable of bringing success to Aberdeen."
On the capture of Twardzik, Fraser added: "Jim Leighton rates the former Bayern Munich goalkeeper very highly and we are delighted to be able to tie this deal up."