Logan's contract was due to expire at the end of the season but he will now remain with the Dons until 2018.
The former Manchester City youngster initially moved to Pittodrie on loan during the 2013-14 season, helping Aberdeen win the League Cup, before signing an initial two-year deal.
The 28-year-old was named in the PFA Scotland Premiership Team of the Year last season and has been a virtual ever-present this year.
Manager Derek McInnes told the club's website: "I was always confident we could try and get there and get a deal done. It is absolutely brilliant news.
"Shay since he came to the club two and a half years ago has been very consistent with his performances and has become a firm favourite with everyone at the club including the supporters.
"I am sure they will be delighted with the news that he has committed himself to us. We are delighted what Shay has given to us over the past two and a half years and delighted to have him for the foreseeable future."
Source: Sky Sports