The club released a statement which revealed that McCall had told board members of his decision late on Sunday afternoon.
Motherwell director Derek Weir said: "Everyone at Motherwell FC would like to sincerely thank Stuart for his contribution to the club, which will go down as one of the most successful managerial tenures in our 128-year history.
"We have been acutely aware of results this season, but everyone at Fir Park was confident in his, and the team's, ability to turn things around.
"However, following a long conversation this afternoon, Stuart felt it better for all concerned if he stepped down with immediate effect and we respect that.
"Assistant manager Kenny Black will take charge of first-team team affairs in a caretaker role to allow the board to start the process of recruiting a new manager, which will begin right away."
McCall will go down as Motherwell's most successful league manager since the Second World War, having secured two runners-up spots, while he is one of only four men to lead them to a Scottish Cup final.
The 50-year-old turned down a number of approaches from Championship clubs in England during his spell at Fir Park and rejected an offer from Sheffield United in the summer of 2013.
McCall recently admitted he felt "a bit lost and helpless" after a 3-1 defeat by Dundee on October 18 but he appeared to have overcome those feelings of doubt following more encouraging performances in the subsequent two games, although the ended in narrow defeats to Aberdeen and St Johnstone.
Motherwell took the lead in Perth on Friday night but missed a chance to score seconds before St Johnstone equalised and an unfortunate slip in defence saw them concede a late winner.
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