The TCDSB did not give a clear reason for its decision in a statement released on its website other than to say it is "pursuing a different direction" and thanked Ford for his commitment to the team.
A spokesman later told CBC News the decision is "in no way related to the current allegations. It is due to the review of his March 1 Sun News Network interview."
John Yan said Ford painted the Don Bosco community negatively when he referred to it as "crime ridden," and the youth as "gang bangers."
- Ford ally says mayor told to limit comments on alleged crack video
The decision comes amid allegations by news gossip website Gawker and the Toronto Star that both claim to have seen a video showing Ford smoking what appears to be crack cocaine.
CBC News has not seen the video and has not been able to validate any of the claims being made.
Bruce Rodriques, the TCDSB's director of education said in the release, "This decision is based on what is best for our students, our school and the Don Bosco community."
Ford will be replaced, the statement said, by "a new volunteer head coach."
The mayor's commitment as volunteer head coach of the north Etobicoke high school football team has not been without controversy.
In November, a TTC bus was diverted off-route to go pick up Don Bosco players at a game after reports that a near brawl was about to break out on the field.
Ford had faced criticism for missing an important council vote to attend the semi-final game that would eventually land the Eagles in the GTA Metro Bowl championship.
"It's the playoffs, we're undefeated, we're No. 2 in the city. We're in the championship game," Ford said later, denying any involvement in requesting the bus.
The Metro Bowl, which Don Bosco would lose to the Huron Heights Warriors, came only a day after a judge ruled the mayor had broken the Municipal Conflict of Interest Act and should be removed from office. A Divisional Court would later overturn the decision allowing Ford to remain in office.
Following the championship game, Ford seemed to imply his plan was to stay on as coach during the 2013 season.
"They're fantastic, I'm not going to turn my back on these kids," Ford said.