Ross left Fir Park in February to pursue other opportunities and was named as Ian Burchnall’s assistant manager at Meadow Lane a month later.
However he has now left his position after admitting making an ‘ill-judged’ comment to one of the playing staff.
The 40-year-old, who has 13 Scotland caps, said: “During Saturday's match at Altrincham, I made an ill-judged comment to a member of our playing staff which has led to my departure from the club.
“I deeply regret the comment, which is not a reflection of the type of person I am, and would like to place on record my apologies to the player in question for the upset I have caused.
"While it was said in the heat of the moment with no malice intended, it was nevertheless unacceptable and I'm devastated by the impact it's caused.
“I would also like to apologise to the club's board of directors, supporters and Ian Burchnall, all of whom I have enjoyed working with immensely.
“The club have handled today's events impeccably and everyone at Meadow Lane has my full support for the rest of the season and beyond.
“I will be taking some time to reflect on my actions and learn from this experience before continuing my coaching journey."
A statement on the Magpies website confirmed the departure: "Assistant head coach Maurice Ross has this afternoon left the club with immediate effect. We will be making no further comment.”
Ross was a highly-rated coach at Fir Park, taking the reserve side and became part of Stephen Robinson’s first-team staff, but left when the Northern Irishman was replaced by Graham Alexander.
He courted controversy earlier this season for comments made surrounding a covid call-off at St Mirren when he called for stiffer punishments for clubs who suffer outbreaks of coronavirus, and St Mirren complained to Motherwell over the radio remarks.
Ross broke through as a player at Rangers under Dick Advocaat before moving to Wolves and Millwall.
He later enjoyed success in Scandinavia before returning to Scotland with Aberdeen and then embarking on a managerial career in the Faroe Islands and Norway.