McCall has had a successful time since arriving at the club in December 2010, securing top six places in the last three seasons, a Scottish Cup Final, and Champions League and Europa League qualification following last season's third place finish.
McCall, whose contract was due to expire at the end of the current season, said: "I am really delighted to have it sorted. As I have said on numerous occasions, there was never any issues, it was just a case of getting round to it.
"I've been doing my job exactly the same in terms of the squad and you have already seen that with some of the younger players who have signed up.
"There has never been any doubt on my mind but I am pleased it is finally signed. We can now focus all the attention on the last seven matches of this SPL season."
Chief Executive Leeann Dempster added: ""We are really delighted to have Stuart at the club for a further two years.
"We have enjoyed real success under his stewardship with a strong backroom staff and playing squad and we hope that we can build on that for the season ahead."