The 31-year-old, whose contract was up in the summer, has made 103 appearances for The Magpies since joining from Aston Villa in 2016.
Clark was part of the Newcastle squad that lifted the Championship title in 2017, a season where the central defender was named the club's Player of the Year.
The Republic of Ireland international has consistently been an important part of Steve Bruce's side this season, appearing 14 times so far, scoring a single goal.
Clark: 'I'm delighted to concentrate now on the next couple of years
Talking to NUFC TV, Clark said: "It's a brilliant feeling and I'm delighted that I've managed to get it signed.
"My contract was ending in the summer; for me, I was trying to stay more focused on the games, getting back involved this season and trying to play games, and I've managed to do that over the last few weeks.
"To be back playing was the real aim for me, then the contract has followed, so I'm delighted to concentrate now on the next couple of years."
Bruce: 'I'm pleased to see his hard work and commitment rewarded'
Head coach Steve Bruce added: "I'm delighted Ciaran has signed a new deal.
"First and foremost, he is a very talented defender and he gives us great balance as a naturally left-footed centre-half.
"He has also become a very consistent performer and I'm pleased to see his hard work and commitment rewarded."