McCall's position had been under scrutiny following the Irish side's 32-14 defeat by Gloucester in the European Cup last week.
The 39-year-old's decision was confirmed at a press conference at Ravenhill on Tuesday morning.
Chief executive Michael Reid said: "Mark McCall tendered his resignation to myself and chairman Cecil Watson yesterday evening.
"The poor results this season have been very difficult for us all and ultimately have brought us to where we are today. However, I believe strongly that the following is recorded:
"Mark McCall has been an outstanding committed coach for Ulster.
"Over the weekend, one paper quite rightly stated, 'If Mark McCall came into work any earlier he would meet himself leaving'. His drive, passion and enthusiasm for Ulster Rugby is immense.
"Mark McCall took on this job at a time when there was little money available in comparison to England and France. He has worked hard to deliver a competitive team on what has not been a level playing field.
"The undoubted highlight of Mark's tenure was our Celtic League win in 2006, such a success over a full season of rugby was a remarkable feather in his cap, and a personal success of which he was justifiably proud."
Former Ireland centre McCall captained during the early part of their European Cup-winning campaign in 1999 until a neck injury forced him to retire prematurely from the game.
He was immediately drafted into the coaching set-up and then worked with Ireland A and Ireland Under-21s before being named Ulster boss in July 2004.
McCall said: "Over the last three-and-a-half years it has been an absolute privilege for me to have been coach of the Ulster rugby team.
"Winning the Celtic League two seasons ago was a huge highlight and it has been very rewarding to watch the Ulster representation in the Irish squad rise year on year."
Wales centre Jonathan Davies admits he is yet to fully come to terms with his devastation after club side Clermont Auvergne suffered a heartbreaking loss in their European final with Toulon on Saturday.